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1.  QTL mapping and epistatic interaction analysis in asparagus bean for several characterized and novel horticulturally important traits 
BMC Genetics  2013;14:4.
Background
Asparagus bean (Vigna. unguiculata. ssp sesquipedalis) is a subspecies and special vegetable type of cowpea (Vigna. unguiculata L. Walp.) important in Asia. Genetic basis of horticulturally important traits of asparagus bean is still poorly understood, hindering the utilization of targeted, DNA marker-assisted breeding in this crop. Here we report the identification of quantitative trait loci (QTLs) and epistatic interactions for four horticultural traits, namely, days to first flowering (FLD), nodes to first flower (NFF), leaf senescence (LS) and pod number per plant (PN) using a recombinant inbred line (RIL) population of asparagus bean.
Results
A similar genetic mode of one major QTL plus a few minor QTLs was found to dominate each of the four traits, with the number of QTLs for individual traits ranging from three to four. These QTLs were distributed on 7 of the 11 chromosomes. Major QTLs for FLD, NFF and LS were co-localized on LG 11, indicative of tight linkage. Genome wide epistasis analysis detected two and one interactive locus pairs that significantly affect FLD and LS, respectively, and the epistatic QTLs for FLD appeared to work in different ways. Synteny based comparison of QTL locations revealed conservation of chromosome regions controlling these traits in related legume crops.
Conclusion
Major, minor, and epistatic QTLs were found to contribute to the inheritance of the FLD, NFF, LS, and PN. Positions of many of these QTLs are conserved among closely related legume species, indicating common mechanisms they share. To our best knowledge, this is the first QTL mapping report using an asparagus bean × asparagus bean intervarietal population and provides marker-trait associations for marker-assisted approaches to selection.
doi:10.1186/1471-2156-14-4
PMCID: PMC3616928  PMID: 23375055
Asparagus bean; Cowpea; Epistasis; Flowering time; Leaf senescence; Node to first flower; Pod number; QTL; RIL
2.  Multienvironment Quantitative Trait Loci Analysis for Photosynthate Acquisition, Accumulation, and Remobilization Traits in Common Bean Under Drought Stress 
G3: Genes|Genomes|Genetics  2012;2(5):579-595.
Many of the world’s common bean (Phaseolus vulgaris L.) growing regions are prone to either intermittent or terminal drought stress, making drought the primary cause of yield loss under farmers’ field conditions. Improved photosynthate acquisition, accumulation, and then remobilization have been observed as important mechanisms for adaptation to drought stress. The objective of this study was to tag quantitative trait loci (QTL) for photosynthate acquisition, accumulation, and remobilization to grain by using a recombinant inbred line population developed from the Mesoamerican intragenepool cross of drought-susceptible DOR364 and drought-tolerant BAT477 grown under eight environments differing in drought stress across two continents: Africa and South America. The recombinant inbred line population expressed quantitative variation and transgressive segregation for 11 traits associated with drought tolerance. QTL were detected by both a mixed multienvironment model and by composite interval mapping for each environment using a linkage map constructed with 165 genetic markers that covered 11 linkage groups of the common bean genome. In the multienvironment, mixed model, nine QTL were detected for 10 drought stress tolerance mechanism traits found on six of the 11 linkage groups. Significant QTL × environment interaction was observed for six of the nine QTL. QTL × environment interaction was of the cross-over type for three of the six significant QTL with contrasting effect of the parental alleles across different environments. In the composite interval mapping, we found 69 QTL in total. The majority of these were found for Palmira (47) or Awassa (18), with fewer in Malawi (4). Phenotypic variation explained by QTL in single environments ranged up to 37%, and the most consistent QTL were for Soil Plant Analysis Development (SPAD) leaf chlorophyll reading and pod partitioning traits. QTL alignment between the two detection methods showed that yield QTL on b08 and stem carbohydrate QTL on b05 were most consistent between the multilocation model and the single environment detection. Our results indicate the relevance of QTL detection in the sites in which bean breeding will be undertaken and the importance of photosynthate accumulation as a trait for common bean drought tolerance.
doi:10.1534/g3.112.002303
PMCID: PMC3362941  PMID: 22670228
biomass partitioning; leaf area and chlorophyll content; QTL × environment interaction; nonstructural carbohydrates; photosynthate remobilization and grain yield
3.  Variation and inheritance of iron reductase activity in the roots of common bean (Phaseolus vulgaris L.) and association with seed iron accumulation QTL 
BMC Plant Biology  2010;10:215.
Background
Iron deficiency anemia is a global problem which often affects women and children of developing countries. Strategy I plants, such as common bean (Phaseolus vulgaris L.) take up iron through a process that involves an iron reduction mechanism in their roots; this reduction is required to convert ferric iron to ferrous iron. Root absorbed iron is critical for the iron nutrition of the plant, and for the delivery of iron to the shoot and ultimately the seeds. The objectives of this study were to determine the variability and inheritance for iron reductase activity in a range of genotypes and in a low × high seed iron cross (DOR364 × G19833), to identify quantitative trait loci (QTL) for this trait, and to assess possible associations with seed iron levels.
Results
The experiments were carried out with hydroponically grown plants provided different amounts of iron varying between 0 and 20 μM Fe(III)-EDDHA. The parents, DOR364 and G19833, plus 13 other cultivated or wild beans, were found to differ in iron reductase activity. Based on these initial experiments, two growth conditions (iron limited and iron sufficient) were selected as treatments for evaluating the DOR364 × G19833 recombinant inbred lines. A single major QTL was found for iron reductase activity under iron-limited conditions (1 μM Fe) on linkage group b02 and another major QTL was found under iron sufficient conditions (15 μM Fe) on linkage group b11. Associations between the b11 QTL were found with several QTL for seed iron.
Conclusions
Genes conditioning iron reductase activity in iron sufficient bean plants appear to be associated with genes contributing to seed iron accumulation. Markers for bean iron reductase (FRO) homologues were found with in silico mapping based on common bean synteny with soybean and Medicago truncatula on b06 and b07; however, neither locus aligned with the QTL for iron reductase activity. In summary, the QTL for iron reductase activity under iron limited conditions may be useful in environments where beans are grown in alkaline soils, while the QTL for iron reductase under sufficiency conditions may be useful for selecting for enhanced seed nutritional quality.
doi:10.1186/1471-2229-10-215
PMCID: PMC3095315  PMID: 20923552
4.  Mapping of angular leaf spot resistance QTL in common bean (Phaseolus vulgaris L.) under different environments 
BMC Genetics  2012;13:50.
Background
Common bean (Phaseolus vulgaris L.) is the most important grain legume for human diet worldwide and the angular leaf spot (ALS) is one of the most devastating diseases of this crop, leading to yield losses as high as 80%. In an attempt to breed resistant cultivars, it is important to first understand the inheritance mode of resistance and to develop tools that could be used in assisted breeding. Therefore, the aim of this study was to identify quantitative trait loci (QTL) controlling resistance to ALS under natural infection conditions in the field and under inoculated conditions in the greenhouse.
Results
QTL analyses were made using phenotypic data from 346 recombinant inbreed lines from the IAC-UNA x CAL 143 cross, gathered in three experiments, two of which were conducted in the field in different seasons and one in the greenhouse. Joint composite interval mapping analysis of QTL x environment interaction was performed. In all, seven QTLs were mapped on five linkage groups. Most of them, with the exception of two, were significant in all experiments. Among these, ALS10.1DG,UC presented major effects (R2 between 16% - 22%). This QTL was found linked to the GATS11b marker of linkage group B10, which was consistently amplified across a set of common bean lines and was associated with the resistance. Four new QTLs were identified. Between them the ALS5.2 showed an important effect (9.4%) under inoculated conditions in the greenhouse. ALS4.2 was another major QTL, under natural infection in the field, explaining 10.8% of the variability for resistance reaction. The other QTLs showed minor effects on resistance.
Conclusions
The results indicated a quantitative inheritance pattern of ALS resistance in the common bean line CAL 143. QTL x environment interactions were observed. Moreover, the major QTL identified on linkage group B10 could be important for bean breeding, as it was stable in all the environments. Thereby, the GATS11b marker is a potential tool for marker assisted selection for ALS resistance.
doi:10.1186/1471-2156-13-50
PMCID: PMC3464175  PMID: 22738188
Phaseolus vulgaris L.; Angular leaf spot; Joint composite interval mapping; CIM; Resistance QTL
5.  The genetics of domestication of rice bean, Vigna umbellata 
Annals of Botany  2010;106(6):927-944.
Background and Aims
The Asian genus Vigna, to which four cultivated species (rice bean, azuki bean, mung bean and black gram) belong, is suitable for comparative genomics. The aims were to construct a genetic linkage map of rice bean, to identify the genomic regions associated with domestication in rice bean, and to compare these regions with those in azuki bean.
Methods
A genetic linkage map was constructed by using simple sequence repeat and amplified fragment length polymorphism markers in the BC1F1 population derived from a cross between cultivated and wild rice bean. Using this map, 31 domestication-related traits were dissected into quantitative trait loci (QTLs). The genetic linkage map and QTLs of rice bean were compared with those of azuki bean.
Key Results
A total of 326 markers converged into 11 linkage groups (LGs), corresponding to the haploid number of rice bean chromosomes. The domestication-related traits in rice bean associated with a few major QTLs distributed as clusters on LGs 2, 4 and 7. A high level of co-linearity in marker order between the rice bean and azuki bean linkage maps was observed. Major QTLs in rice bean were found on LG4, whereas major QTLs in azuki bean were found on LG9.
Conclusions
This is the first report of a genetic linkage map and QTLs for domestication-related traits in rice bean. The inheritance of domestication-related traits was so simple that a few major QTLs explained the phenotypic variation between cultivated and wild rice bean. The high level of genomic synteny between rice bean and azuki bean facilitates QTL comparison between species. These results provide a genetic foundation for improvement of rice bean; interchange of major QTLs between rice bean and azuki bean might be useful for broadening the genetic variation of both species.
doi:10.1093/aob/mcq188
PMCID: PMC2990660  PMID: 20880934
Rice bean; Vigna umbellata; azuki bean; comparative genomics; SSR; domestication; wild species; QTL
6.  The genetics of domestication of yardlong bean, Vigna unguiculata (L.) Walp. ssp. unguiculata cv.-gr. sesquipedalis 
Annals of Botany  2012;109(6):1185-1200.
Background and Aims
The genetics of domestication of yardlong bean [Vigna unguiculata (L.) Walp. ssp. unguiculata cv.-gr. sesquipedalis] is of particular interest because the genome of this legume has experienced divergent domestication. Initially, cowpea was domesticated from wild cowpea in Africa; in Asia a vegetable form of cowpea, yardlong bean, subsequently evolved from cowpea. Information on the genetics of domestication-related traits would be useful for yardlong bean and cowpea breeding programmes, as well as comparative genome study among members of the genus Vigna. The objectives of this study were to identify quantitative trait loci (QTLs) for domestication-related traits in yardlong bean and compare them with previously reported QTLs in closely related Vigna.
Methods
Two linkage maps were developed from BC1F1 and F2 populations from the cross between yardlong bean (V. unguiculata ssp. unguiculata cv.-gr. sesquipedalis) accession JP81610 and wild cowpea (V. unguiculata ssp. unguiculata var. spontanea) accession TVnu457. Using these linkage maps, QTLs for 24 domestication-related traits were analysed and mapped. QTLs were detected for traits related to seed, pod, stem and leaf.
Key Results
Most traits were controlled by between one and 11 QTLs. QTLs for domestication-related traits show co-location on several narrow genomic regions on almost all linkage groups (LGs), but especially on LGs 3, 7, 8 and 11. Major QTLs for sizes of seed, pod, stem and leaf were principally located on LG7. Pleiotropy or close linkage of genes for the traits is suggested in these chromosome regions.
Conclusions
This is the first report of QTLs for domestication-related traits in yardlong bean. The results provide a foundation for marker-assisted selection of domestication-related QTLs in yardlong bean and enhance understanding of domestication in the genus Vigna.
doi:10.1093/aob/mcs048
PMCID: PMC3336956  PMID: 22419763
Cowpea; QTL analysis; domestication; Vigna unguiculata; evolution; yardlong bean
7.  Identification of expressed resistance gene-like sequences by data mining in 454-derived transcriptomic sequences of common bean (Phaseolus vulgaris L.) 
BMC Plant Biology  2012;12:42.
Background
Common bean (Phaseolus vulgaris L.) is one of the most important legumes in the world. Several diseases severely reduce bean production and quality; therefore, it is very important to better understand disease resistance in common bean in order to prevent these losses. More than 70 resistance (R) genes which confer resistance against various pathogens have been cloned from diverse plant species. Most R genes share highly conserved domains which facilitates the identification of new candidate R genes from the same species or other species. The goals of this study were to isolate expressed R gene-like sequences (RGLs) from 454-derived transcriptomic sequences and expressed sequence tags (ESTs) of common bean, and to develop RGL-tagged molecular markers.
Results
A data-mining approach was used to identify tentative P. vulgaris R gene-like sequences from approximately 1.69 million 454-derived sequences and 116,716 ESTs deposited in GenBank. A total of 365 non-redundant sequences were identified and named as common bean (P. vulgaris = Pv) resistance gene-like sequences (PvRGLs). Among the identified PvRGLs, about 60% (218 PvRGLs) were from 454-derived sequences. Reverse transcriptase-polymerase chain reaction (RT-PCR) analysis confirmed that PvRGLs were actually expressed in the leaves of common bean. Upon comparison to P. vulgaris genomic sequences, 105 (28.77%) of the 365 tentative PvRGLs could be integrated into the existing common bean physical map. Based on the syntenic blocks between common bean and soybean, 237 (64.93%) PvRGLs were anchored on the P. vulgaris genetic map and will need to be mapped to determine order. In addition, 11 sequence-tagged-site (STS) and 19 cleaved amplified polymorphic sequence (CAPS) molecular markers were developed for 25 unique PvRGLs.
Conclusions
In total, 365 PvRGLs were successfully identified from 454-derived transcriptomic sequences and ESTs available in GenBank and about 65% of PvRGLs were integrated into the common bean genetic map. A total of 30 RGL-tagged markers were developed for 25 unique PvRGLs, including 11 STS and 19 CAPS markers. The expressed PvRGLs identified in this study provide a large sequence resource for development of RGL-tagged markers that could be used further for genetic mapping of disease resistant candidate genes and quantitative trait locus/loci (QTLs). This work also represents an additional method for identifying expressed RGLs from next generation sequencing data.
doi:10.1186/1471-2229-12-42
PMCID: PMC3353201  PMID: 22443214
Common bean (Phaseolus vulgaris L.); 454 pyrosequencing; ESTs; Resistance gene-like sequences; Molecular markers
8.  A reference consensus genetic map for molecular markers and economically important traits in faba bean (Vicia faba L.) 
BMC Genomics  2013;14:932.
Background
Faba bean (Vicia faba L.) is among the earliest domesticated crops from the Near East. Today this legume is a key protein feed and food worldwide and continues to serve an important role in culinary traditions throughout Middle East, Mediterranean region, China and Ethiopia. Adapted to a wide range of soil types, the main faba bean breeding objectives are to improve yield, resistance to biotic and abiotic stresses, seed quality and other agronomic traits. Genomic approaches aimed at enhancing faba bean breeding programs require high-quality genetic linkage maps to facilitate quantitative trait locus analysis and gene tagging for use in a marker-assisted selection. The objective of this study was to construct a reference consensus map in faba bean by joining the information from the most relevant maps reported so far in this crop.
Results
A combination of two approaches, increasing the number of anchor loci in diverse mapping populations and joining the corresponding genetic maps, was used to develop a reference consensus map in faba bean. The map was constructed from three main recombinant inbreed populations derived from four parental lines, incorporates 729 markers and is based on 69 common loci. It spans 4,602 cM with a range from 323 to 1041 loci in six main linkage groups or chromosomes, and an average marker density of one locus every 6 cM. Locus order is generally well maintained between the consensus map and the individual maps.
Conclusion
We have constructed a reliable and fairly dense consensus genetic linkage map that will serve as a basis for genomic approaches in faba bean research and breeding. The core map contains a larger number of markers than any previous individual map, covers existing gaps and achieves a wider coverage of the large faba bean genome as a whole. This tool can be used as a reference resource for studies in different genetic backgrounds, and provides a framework for transferring genetic information when using different marker technologies. Combined with syntenic approaches, the consensus map will increase marker density in selected genomic regions and will be useful for future faba bean molecular breeding applications.
doi:10.1186/1471-2164-14-932
PMCID: PMC3880837  PMID: 24377374
Faba bean; Consensus map; Gene based markers; Quantitative trait loci; Comparative mapping; Molecular breeding; Marker-assisted selection; Genomics
9.  Association mapping of common bacterial blight resistance QTL in Ontario bean breeding populations 
BMC Plant Biology  2011;11:52.
Background
Common bacterial blight (CBB), incited by Xanthomonas axonopodis pv. phaseoli (Xap), is a major yield-limiting factor of common bean (Phaseolus vulgaris L.) production around the world. Host resistance is practically the most effective and environmentally-sound approach to control CBB. Unlike conventional QTL discovery strategies, in which bi-parental populations (F2, RIL, or DH) need to be developed, association mapping-based strategies can use plant breeding populations to synchronize QTL discovery and cultivar development.
Results
A population of 469 dry bean lines of different market classes representing plant materials routinely developed in a bean breeding program were used. Of them, 395 lines were evaluated for CBB resistance at 14 and 21 DAI (Days After Inoculation) in the summer of 2009 in an artificially inoculated CBB nursery in south-western Ontario. All lines were genotyped using 132 SNPs (Single Nucleotide Polymorphisms) evenly distributed across the genome. Of the 132 SNPs, 26 SNPs had more than 20% missing data, 12 SNPs were monomorphic, and 17 SNPs had a MAF (Minor Allelic Frequency) of less than 0.20, therefore only 75 SNPs were used for association study, based on one SNP per locus. The best possible population structure was to assign 36% and 64% of the lines into Andean and Mesoamerican subgroups, respectively. Kinship analysis also revealed complex familial relationships among all lines, which corresponds with the known pedigree history. MLM (Mixed Linear Model) analysis, including population structure and kinship, was used to discover marker-trait associations. Eighteen and 22 markers were significantly associated with CBB rating at 14 and 21 DAI, respectively. Fourteen markers were significant for both dates and the markers UBC420, SU91, g321, g471, and g796 were highly significant (p ≤ 0.001). Furthermore, 12 significant SNP markers were co-localized with or close to the CBB-QTLs identified previously in bi-parental QTL mapping studies.
Conclusions
This study demonstrated that association mapping using a reasonable number of markers, distributed across the genome and with application of plant materials that are routinely developed in a plant breeding program can detect significant QTLs for traits of interest.
doi:10.1186/1471-2229-11-52
PMCID: PMC3078875  PMID: 21435233
10.  Development of a Mesoamerican intra-genepool genetic map for quantitative trait loci detection in a drought tolerant × susceptible common bean (Phaseolus vulgaris L.) cross 
Molecular Breeding  2010;29(1):71-88.
Drought is a major constraint to common bean (Phaseolus vulgaris L.) production, especially in developing countries where irrigation for the crop is infrequent. The Mesoamerican genepool is the most widely grown subdivision of common beans that include small red, small cream and black seeded varieties. The objective of this study was to develop a reliable genetic map for a Mesoamerican × Mesoamerican drought tolerant × susceptible cross and to use this map to analyze the inheritance of yield traits under drought and fully irrigated conditions over 3 years of experiments. The source of drought tolerance used in the cross was the cream-seeded advanced line BAT477 crossed with the small red variety DOR364 and the population was made up of recombinant inbred lines in the F5 generation. Quantitative trait loci were detected by composite interval mapping for the traits of overall seed yield, yield per day, 100 seed weight, days to flowering and days to maturity for each field environment consisting of two treatments (irrigated and rainfed) and lattice design experiments with three repetitions for a total of six environments. The genetic map based on amplified fragment length polymorphism and random amplified polymorphic DNA markers was anchored with 60 simple sequence repeat (SSR) markers and had a total map length of 1,087.5 cM across 11 linkage groups covering the whole common bean genome with saturation of one marker every 5.9 cM. Gaps for the genetic map existed on linkage groups b03, b09 and b11 but overall there were only nine gaps larger than 15 cM. All traits were inherited quantitatively, with the greatest number for seed weight followed by yield per day, yield per se, days to flowering and days to maturity. The relevance of these results for breeding common beans is discussed in particular in the light of crop improvement for drought tolerance in the Mesoamerican genepool.
doi:10.1007/s11032-010-9527-9
PMCID: PMC3253996  PMID: 22267950
Drought stress; Field tolerance mechanisms; Quantitative trait loci; Seed yield
11.  Genetic architecture of complex agronomic traits examined in two testcross populations of rye (Secale cereale L.) 
BMC Genomics  2012;13:706.
Background
Rye is an important European crop used for food, feed, and bioenergy. Several quality and yield-related traits are of agronomic relevance for rye breeding programs. Profound knowledge of the genetic architecture of these traits is needed to successfully implement marker-assisted selection programs. Nevertheless, little is known on quantitative loci underlying important agronomic traits in rye.
Results
We used 440 F3:4 inbred lines from two biparental populations (Pop-A, Pop-B) fingerprinted with about 800 to 900 SNP, SSR and/or DArT markers and outcrossed them to a tester for phenotyping. The resulting hybrids and their parents were evaluated for grain yield, single-ear weight, test weight, plant height, thousand-kernel weight, falling number, protein, starch, soluble and total pentosan contents in up to ten environments in Central Europe. The quality of the phenotypic data was high reflected by moderate to high heritability estimates. QTL analyses revealed a total of 31 QTL for Pop-A and 52 for Pop-B. QTL x environment interactions were significant (P < 0.01) in most cases but variance of QTL main effect was more prominent.
Conclusions
QTL mapping was successfully applied based on two segregating rye populations. QTL underlying grain yield and several quality traits had small effects. In contrast, thousand-kernel weight, test weight, falling number and starch content were affected by several major QTL with a high frequency of occurrence in cross validation. These QTL explaining a large proportion of the genotypic variance can be exploited in marker-assisted selection programs and are candidates for further genetic dissection.
doi:10.1186/1471-2164-13-706
PMCID: PMC3566906  PMID: 23244545
12.  Genome Dissection of Traits Related to Domestication in Azuki Bean (Vigna angularis) and Comparison with other Warm-season Legumes 
Annals of Botany  2007;100(5):1053-1071.
Background
The objective of this study was to dissect into quantitative trait loci (QTLs) the large morphological and physiological differences between cultivated azuki bean (Vigna angularis) and a wild relative and to infer the commonalities of the QTLs for domestication-related traits across the Asian Vigna and with other warm-season legumes.
Methods
Two linkage maps, for the BC1F1 and F2 populations, respectively, from the same cross between azuki bean and V. nepalensis were developed. Using these linkage maps QTLs for 33 domestication-related traits were analysed and mapped. The location of mapped QTLs was compared with locations of similar QTLs in other warm-season legumes.
Key Results
QTLs were detected for seed-, pod-, stem- and leaf-related traits. Most traits were controlled by between two and nine QTLs but several traits, such as pod dehiscence, were controlled by single genes. QTLs for domestication-related traits were restricted to particular regions of the azuki bean genome, especially linkage groups 1, 2, 4, 7 and 9. Linkage groups 1 and 2 had QTLs for a suite of traits including pod size, germination, seed size and lower stem length. QTLs on linkage groups 7 and 9 were associated with upper stem length, maximum leaf size and pod and seed size. Pleiotropy or close linkage of genes for domestication-related traits is suggested in these regions. While some QTLs are common to azuki bean and other warm-season legumes, many are recorded for the first time in azuki bean.
Conclusions
QTLs for a large number of domestication-related traits have been mapped for the first time in azuki bean. QTLs with unexpected effect and new QTLs for traits such as seed size have been found. The results provide a foundation that will be useful for improvement of azuki bean and related legumes.
doi:10.1093/aob/mcm155
PMCID: PMC2759210  PMID: 17728336
Azuki bean; Vigna angularis var. angularis; Vigna nepalensis; wild species; QTL; microsatellite
13.  A fruit quality gene map of Prunus 
BMC Genomics  2009;10:587.
Background
Prunus fruit development, growth, ripening, and senescence includes major biochemical and sensory changes in texture, color, and flavor. The genetic dissection of these complex processes has important applications in crop improvement, to facilitate maximizing and maintaining stone fruit quality from production and processing through to marketing and consumption. Here we present an integrated fruit quality gene map of Prunus containing 133 genes putatively involved in the determination of fruit texture, pigmentation, flavor, and chilling injury resistance.
Results
A genetic linkage map of 211 markers was constructed for an intraspecific peach (Prunus persica) progeny population, Pop-DG, derived from a canning peach cultivar 'Dr. Davis' and a fresh market cultivar 'Georgia Belle'. The Pop-DG map covered 818 cM of the peach genome and included three morphological markers, 11 ripening candidate genes, 13 cold-responsive genes, 21 novel EST-SSRs from the ChillPeach database, 58 previously reported SSRs, 40 RAFs, 23 SRAPs, 14 IMAs, and 28 accessory markers from candidate gene amplification. The Pop-DG map was co-linear with the Prunus reference T × E map, with 39 SSR markers in common to align the maps. A further 158 markers were bin-mapped to the reference map: 59 ripening candidate genes, 50 cold-responsive genes, and 50 novel EST-SSRs from ChillPeach, with deduced locations in Pop-DG via comparative mapping. Several candidate genes and EST-SSRs co-located with previously reported major trait loci and quantitative trait loci for chilling injury symptoms in Pop-DG.
Conclusion
The candidate gene approach combined with bin-mapping and availability of a community-recognized reference genetic map provides an efficient means of locating genes of interest in a target genome. We highlight the co-localization of fruit quality candidate genes with previously reported fruit quality QTLs. The fruit quality gene map developed here is a valuable tool for dissecting the genetic architecture of fruit quality traits in Prunus crops.
doi:10.1186/1471-2164-10-587
PMCID: PMC2797820  PMID: 19995417
14.  Mapping QTLs for oil traits and eQTLs for oleosin genes in jatropha 
BMC Plant Biology  2011;11:132.
Background
The major fatty acids in seed oil of jatropha, a biofuel crop, are palmitic acid (C16:0), stearic acid (C18:0), oleic acid (C18:1) and linoleic acid (C18:2). High oleic acid and total oil content are desirable for jatropha breeding. Until now, little was known about the genetic bases of these oil traits in jatropha. In this study, quantitative trait locus (QTL) and expression QTL analyses were applied to identify genetic factors that are relevant to seed oil traits in jatropha.
Results
Composite interval mapping identified 18 QTL underlying the oil traits. A highly significant QTL qC18:1-1 was detected at one end of linkage group (LG) 1 with logarithm of the odd (LOD) 18.4 and percentage of variance explained (PVE) 36.0%. Interestingly, the QTL qC18:1-1 overlapped with qC18:2-1, controlling oleic acid and linoleic acid compositions. Among the significant QTL controlling total oil content, qOilC-4 was mapped on LG4 a relatively high significant level with LOD 5.0 and PVE 11.1%. Meanwhile, oleosins are the major composition in oil body affecting oil traits; we therefore developed SNP markers in three oleosin genes OleI, OleII and OleIII, which were mapped onto the linkage map. OleI and OleIII were mapped on LG5, closing to QTLs controlling oleic acid and stearic acid. We further determined the expressions of OleI, OleII and OleIII in mature seeds from the QTL mapping population, and detected expression QTLs (eQTLs) of the three genes on LGs 5, 6 and 8 respectively. The eQTL of OleIII, qOleIII-5, was detected on LG5 with PVE 11.7% and overlapped with QTLs controlling stearic acid and oleic acid, implying a cis- or trans-element for the OleIII affecting fatty acid compositions.
Conclusion
We identified 18 QTLs underlying the oil traits and 3 eQTLs of the oleosin acid genes. The QTLs and eQTLs, especially qC18:1-1, qOilC-4 and qOleIII-5 with contribution rates (R2) higher than 10%, controlling oleic acid, total oil content and oleosin gene expression respectively, will provide indispensable data for initiating molecular breeding to improve seed oil traits in jatropha, the key crop for biodiesel production.
doi:10.1186/1471-2229-11-132
PMCID: PMC3195091  PMID: 21958236
15.  Dissecting tocopherols content in maize (Zea mays L.), using two segregating populations and high-density single nucleotide polymorphism markers 
BMC Plant Biology  2012;12:201.
Background
Tocopherols, which are vitamin E compounds, play an important role in maintaining human health. Compared with other staple foods, maize grains contain high level of tocopherols.
Results
Two F2 populations (K22/CI7 and K22/Dan340, referred to as POP-1 and POP-2, respectively), which share a common parent (K22), were developed and genotyped using a GoldenGate assay containing 1,536 single nucleotide polymorphism (SNP) markers. An integrated genetic linkage map was constructed using 619 SNP markers, spanning a total of 1649.03 cM of the maize genome with an average interval of 2.67 cM. Seventeen quantitative trait loci (QTLs) for all the traits were detected in the first map and 13 in the second. In these two maps, QTLs for different traits were localized to the same genomic regions and some were co-located with candidate genes in the tocopherol biosynthesis pathway. Single QTL was responsible for 3.03% to 52.75% of the phenotypic variation and the QTLs in sum explained23.4% to 66.52% of the total phenotypic variation. A major QTL (qc5-1/qd5-1) affecting α-tocopherol (αT) was identified on chromosome 5 between the PZA03161.1 and PZA02068.1 in the POP-2. The QTL region was narrowed down from 18.7 Mb to 5.4 Mb by estimating the recombination using high-density markers of the QTL region. This allowed the identification of the candidate gene VTE4 which encodes γ-tocopherol methyltransferase, an enzyme that transforms γ-tocopherol (γT)to αT.
Conclusions
These results demonstrate that a few QTLs with major effects and several QTLs with medium to minor effects might contribute to the natural variation of tocopherols in maize grain. The high-density markers will help to fine map and identify the QTLs with major effects even in the preliminary segregating populations. Furthermore, this study provides a simple guide line for the breeders to improve traits that minimize the risk of malnutrition, especially in developing countries.
doi:10.1186/1471-2229-12-201
PMCID: PMC3502391  PMID: 23122295
Maize; Tocopherols; QTL mapping
16.  A legume biofortification quandary: variability and genetic control of seed coat micronutrient accumulation in common beans 
Common beans (Phaseolus vulgaris L.), like many legumes, are rich in iron, zinc, and certain other microelements that are generally found to be in low concentrations in cereals, other seed crops, and root or tubers and therefore are good candidates for biofortification. But a quandary exists in common bean biofortification: namely that the distribution of iron has been found to be variable between the principal parts of seed; namely the cotyledonary tissue, embryo axis and seed coat. The seed coat represents ten or more percent of the seed weight and must be considered specifically as it accumulates much of the anti-nutrients such as tannins that effect mineral bioavailability. Meanwhile the cotyledons accumulate starch and phosphorus in the form of phytates. The goal of this study was to evaluate a population of progeny derived from an advanced backcross of a wild bean and a cultivated Andean bean for seed coat versus cotyledonary minerals to identify variability and predict inheritance of the minerals. We used wild common beans because of their higher seed mineral concentration compared to cultivars and greater proportion of seed coat to total seed weight. Results showed the most important gene for seed coat iron was on linkage group B04 but also identified other QTL for seed coat and cotyledonary iron and zinc on other linkage groups, including B11 which has been important in studies of whole seed. The importance of these results in terms of physiology, candidate genes and plant breeding are discussed.
doi:10.3389/fpls.2013.00275
PMCID: PMC3725406  PMID: 23908660
advanced backcross breeding method; cotyledon; embryo axis; iron and zinc concentration; use of wild beans; seed coat
17.  New stable QTLs for berry weight do not colocalize with QTLs for seed traits in cultivated grapevine (Vitis vinifera L.) 
BMC Plant Biology  2013;13:217.
Background
In grapevine, as in other fruit crops, fruit size and seed content are key components of yield and quality; however, very few Quantitative Trait Loci (QTLs) for berry weight and seed content (number, weight, and dry matter percentage) have been discovered so far. To identify new stable QTLs for marker-assisted selection and candidate gene identification, we performed simultaneous QTL detection in four mapping populations (seeded or seedless) with various genetic backgrounds.
Results
For berry weight, we identified five new QTLs, on linkage groups (LGs) 1, 8, 11, 17 and 18, in addition to the known major QTL on LG 18. The QTL with the largest effect explained up to 31% of total variance and was found in two genetically distant populations on LG 17, where it colocalized with a published putative domestication locus. For seed traits, besides the major QTLs on LG 18 previously reported, we found four new QTLs explaining up to 51% of total variance, on LGs 4, 5, 12 and 14. The previously published QTL for seed number on LG 2 was found related in fact to sex. We found colocalizations between seed and berry weight QTLs only for the major QTL on LG 18 in a seedless background, and on LGs 1 and 13 in a seeded background. Candidate genes belonging to the cell number regulator CNR or cytochrome P450 families were found under the berry weight QTLs on LGs 1, 8, and 17. The involvement of these gene families in fruit weight was first described in tomato using a QTL-cloning approach. Several other interesting candidate genes related to cell wall modifications, water import, auxin and ethylene signalling, transcription control, or organ identity were also found under berry weight QTLs.
Conclusion
We discovered a total of nine new QTLs for berry weight or seed traits in grapevine, thereby increasing more than twofold the number of reliable QTLs for these traits available for marker assisted selection or candidate gene studies. The lack of colocalization between berry and seed QTLs suggests that these traits may be partly dissociated.
doi:10.1186/1471-2229-13-217
PMCID: PMC3878267  PMID: 24350702
Berry weight; Candidate gene; Grapevine; Quantitative trait locus; QTL; Seed number; Seed weight; Vitis vinifera
18.  Genetic Architecture of Delayed Senescence, Biomass, and Grain Yield under Drought Stress in Cowpea 
PLoS ONE  2013;8(7):e70041.
The stay-green phenomenon is a key plant trait with wide usage in managing crop production under limited water conditions. This trait enhances delayed senescence, biomass, and grain yield under drought stress. In this study we sought to identify QTLs in cowpea (Vigna unguiculata) consistent across experiments conducted in Burkina Faso, Nigeria, Senegal, and the United States of America under limited water conditions. A panel of 383 diverse cowpea accessions and a recombinant inbred line population (RIL) were SNP genotyped using an Illumina 1536 GoldenGate assay. Phenotypic data from thirteen experiments conducted across the four countries were used to identify SNP-trait associations based on linkage disequilibrium association mapping, with bi-parental QTL mapping as a complementary strategy. We identified seven loci, five of which exhibited evidence suggesting pleiotropic effects (stay-green) between delayed senescence, biomass, and grain yield. Further, we provide evidence suggesting the existence of positive pleiotropy in cowpea based on positively correlated mean phenotypic values (0.34< r <0.87) and allele effects (0.07< r <0.86) for delayed senescence and grain yield across three African environments. Three of the five putative stay-green QTLs, Dro-1, 3, and 7 were identified in both RILs and diverse germplasm with resolutions of 3.2 cM or less for each of the three loci, suggesting that these may be valuable targets for marker-assisted breeding in cowpea. Also, the co-location of early vegetative delayed senescence with biomass and grain yield QTLs suggests the possibility of using delayed senescence at the seedling stage as a rapid screening tool for post-flowering drought tolerance in cowpea breeding. BLAST analysis using EST sequences harboring SNPs with the highest associations provided a genomic context for loci identified in this study in closely related common bean (Phaseolus vulgaris) and soybean (Glycine max) reference genomes.
doi:10.1371/journal.pone.0070041
PMCID: PMC3728364  PMID: 23936140
19.  Identifying the genetic determinants of transcription factor activity 
Genome-wide messenger RNA expression levels are highly heritable. However, the molecular mechanisms underlying this heritability are poorly understood.The influence of trans-acting polymorphisms is often mediated by changes in the regulatory activity of one or more sequence-specific transcription factors (TFs). We use a method that exploits prior information about the DNA-binding specificity of each TF to estimate its genotype-specific regulatory activity. To this end, we perform linear regression of genotype-specific differential mRNA expression on TF-specific promoter-binding affinity.Treating inferred TF activity as a quantitative trait and mapping it across a panel of segregants from an experimental genetic cross allows us to identify trans-acting loci (‘aQTLs') whose allelic variation modulates the TF. A few of these aQTL regions contain the gene encoding the TF itself; several others contain a gene whose protein product is known to interact with the TF.Our method is strictly causal, as it only uses sequence-based features as predictors. Application to budding yeast demonstrates a dramatic increase in statistical power, compared with existing methods, to detect locus-TF associations and trans-acting loci. Our aQTL mapping strategy also succeeds in mouse.
Genetic sequence variation naturally perturbs mRNA expression levels in the cell. In recent years, analysis of parallel genotyping and expression profiling data for segregants from genetic crosses between parental strains has revealed that mRNA expression levels are highly heritable. Expression quantitative trait loci (eQTLs), whose allelic variation regulates the expression level of individual genes, have successfully been identified (Brem et al, 2002; Schadt et al, 2003). The molecular mechanisms underlying the heritability of mRNA expression are poorly understood. However, they are likely to involve mediation by transcription factors (TFs). We present a new transcription-factor-centric method that greatly increases our ability to understand what drives the genetic variation in mRNA expression (Figure 1). Our method identifies genomic loci (‘aQTLs') whose allelic variation modulates the protein-level activity of specific TFs. To map aQTLs, we integrate genotyping and expression profiling data with quantitative prior information about DNA-binding specificity of transcription factors in the form of position-specific affinity matrices (Bussemaker et al, 2007). We applied our method in two different organisms: budding yeast and mouse.
In our approach, the inferred TF activity is explicitly treated as a quantitative trait, and genetically mapped. The decrease of ‘phenotype space' from that of all genes (in the eQTL approach) to that of all TFs (in our aQTL approach) increases the statistical power to detect trans-acting loci in two distinct ways. First, as each inferred TF activity is derived from a large number of genes, it is far less noisy than mRNA levels of individual genes. Second, the number of trait/marker combinations that needs to be tested for statistical significance in parallel is roughly two orders of magnitude smaller than for eQTLs. We identified a total of 103 locus-TF associations, a more than six-fold improvement over the 17 locus-TF associations identified by several existing methods (Brem et al, 2002; Yvert et al, 2003; Lee et al, 2006; Smith and Kruglyak, 2008; Zhu et al, 2008). The total number of distinct genomic loci identified as an aQTL equals 31, which includes 11 of the 13 previously identified eQTL hotspots (Smith and Kruglyak, 2008).
To better understand the mechanisms underlying the identified genetic linkages, we examined the genes within each aQTL region. First, we found four ‘local' aQTLs, which encompass the gene encoding the TF itself. This includes the known polymorphism in the HAP1 gene (Brem et al, 2002), but also novel predictions of trans-acting polymorphisms in RFX1, STB5, and HAP4. Second, using high-throughput protein–protein interaction data, we identified putative causal genes for several aQTLs. For example, we predict that a polymorphism in the cyclin-dependent kinase CDC28 antagonistically modulates the functionally distinct cell cycle regulators Fkh1 and Fkh2. In this and other cases, our approach naturally accounts for post-translational modulation of TF activity at the protein level.
We validated our ability to predict locus-TF associations in yeast using gene expression profiles of allele replacement strains from a previous study (Smith and Kruglyak, 2008). Chromosome 15 contains an aQTL whose allelic status influences the activity of no fewer than 30 distinct TFs. This locus includes IRA2, which controls intracellular cAMP levels. We used the gene expression profile of IRA2 replacement strains to confirm that the polymorphism within IRA2 indeed modulates a subset of the TFs whose activity was predicted to link to this locus, and no other TFs.
Application of our approach to mouse data identified an aQTL modulating the activity of a specific TF in liver cells. We identified an aQTL on mouse chromosome 7 for Zscan4, a transcription factor containing four zinc finger domains and a SCAN domain. Even though we could not detect a candidate causal gene for Zscan4p because of lack of information about the mouse genome, our result demonstrates that our method also works in higher eukaryotes.
In summary, aQTL mapping has a greatly improved sensitivity to detect molecular mechanisms underlying the heritability of gene expression. The successful application of our approach to yeast and mouse data underscores the value of explicitly treating the inferred TF activity as a quantitative trait for increasing statistical power of detecting trans-acting loci. Furthermore, our method is computationally efficient, and easily applicable to any other organism whenever prior information about the DNA-binding specificity of TFs is available.
Analysis of parallel genotyping and expression profiling data has shown that mRNA expression levels are highly heritable. Currently, only a tiny fraction of this genetic variance can be mechanistically accounted for. The influence of trans-acting polymorphisms on gene expression traits is often mediated by transcription factors (TFs). We present a method that exploits prior knowledge about the in vitro DNA-binding specificity of a TF in order to map the loci (‘aQTLs') whose inheritance modulates its protein-level regulatory activity. Genome-wide regression of differential mRNA expression on predicted promoter affinity is used to estimate segregant-specific TF activity, which is subsequently mapped as a quantitative phenotype. In budding yeast, our method identifies six times as many locus-TF associations and more than twice as many trans-acting loci as all existing methods combined. Application to mouse data from an F2 intercross identified an aQTL on chromosome VII modulating the activity of Zscan4 in liver cells. Our method has greatly improved statistical power over existing methods, is mechanism based, strictly causal, computationally efficient, and generally applicable.
doi:10.1038/msb.2010.64
PMCID: PMC2964119  PMID: 20865005
gene expression; gene regulatory networks; genetic variation; quantitative trait loci; transcription factors
20.  QTL Mapping of Domestication-related Traits in Soybean (Glycine max) 
Annals of Botany  2007;100(5):1027-1038.
Background and Aims
Understanding the genetic basis underlying domestication-related traits (DRTs) is important in order to use wild germplasm efficiently for improving yield, stress tolerance and quality of crops. This study was conducted to characterize the genetic basis of DRTs in soybean (Glycine max) using quantitative trait locus (QTL) mapping.
Methods
A population of 96 recombinant inbred lines derived from a cultivated (ssp. max) × wild (ssp. soja) cross was used for mapping and QTL analysis. Nine DRTs were examined in 2004 and 2005. A linkage map was constructed with 282 markers by the Kosambi function, and the QTL was detected by composite interval mapping.
Key Results
The early flowering and determinate habit derived from the max parent were each controlled by one major QTL, corresponding to the major genes for maturity (e1) and determinate habit (dt1), respectively. There were only one or two significant QTLs for twinning habit, pod dehiscence, seed weight and hard seededness, which each accounted for approx. 20–50 % of the total variance. A comparison with the QTLs detected previously indicated that in pod dehiscence and hard seededness, at least one major QTL was common across different crosses, whereas no such consistent QTL existed for seed weight.
Conclusions
Most of the DRTs in soybeans were conditioned by one or two major QTLs and a number of genotype-dependent minor QTLs. The common major QTLs identified in pod dehiscence and hard seededness may have been key loci in the domestication of soybean. The evolutionary changes toward larger seed may have occurred through the accumulation of minor changes at many QTLs. Since the major QTLs for DRTs were scattered across only six of the 20 linkage groups, and since the QTLs were not clustered, introgression of useful genes from wild to cultivated soybeans can be carried out without large obstacles.
doi:10.1093/aob/mcm149
PMCID: PMC2759197  PMID: 17684023
Soybean; Glycine max; domestication related traits; QTL; hard seededness; seed size; pod dehiscence; twinning habit
21.  Synteny mapping between common bean and soybean reveals extensive blocks of shared loci 
BMC Genomics  2010;11:184.
Background
Understanding syntentic relationship between two species is critical to assessing the potential for comparative genomic analysis. Common bean (Phaseolus vulgaris L.) and soybean (Glycine max L.), the two most important members of the Phaseoleae legumes, appear to have a diploid and polyploidy recent past, respectively. Determining the syntentic relationship between these two species will allow researchers to leverage not only genomic resources but also genetic data for important agronomic traits to improve both of these species.
Results
Genetically-positioned transcript loci of common bean were mapped relative to the recent soybean 1.01 pseudochromosome assembly. In nearly every case, each common bean locus mapped to two loci in soybean, a result consistent with the duplicate polyploidy history of soybean. Blocks of synteny averaging 32 cM in common bean and 4.9 Mb in soybean were observed for all 11 common bean linkage groups, and these blocks mapped to all 20 soybean pseudochromosomes. The median physical-to-genetic distance ratio in common bean (based on soybean physical distances) was ~120 kb/cM. ~15,000 common bean sequences (primarily EST contigs and EST singletons) were electronically positioned onto the common bean map using the shared syntentic blocks as references points.
Conclusion
The collected evidence from this mapping strongly supports the duplicate history of soybean. It further provides evidence that the soybean genome was fractionated and reassembled at some point following the duplication event. These well mapped syntentic relationships between common bean and soybean will enable researchers to target specific genomic regions to discover genes or loci that affect phenotypic expression in both species.
doi:10.1186/1471-2164-11-184
PMCID: PMC2851600  PMID: 20298570
22.  In silico comparison of genomic regions containing genes coding for enzymes and transcription factors for the phenylpropanoid pathway in Phaseolus vulgaris L. and Glycine max L. Merr 
Legumes contain a variety of phytochemicals derived from the phenylpropanoid pathway that have important effects on human health as well as seed coat color, plant disease resistance and nodulation. However, the information about the genes involved in this important pathway is fragmentary in common bean (Phaseolus vulgaris L.). The objectives of this research were to isolate genes that function in and control the phenylpropanoid pathway in common bean, determine their genomic locations in silico in common bean and soybean, and analyze sequences of the 4CL gene family in two common bean genotypes. Sequences of phenylpropanoid pathway genes available for common bean or other plant species were aligned, and the conserved regions were used to design sequence-specific primers. The PCR products were cloned and sequenced and the gene sequences along with common bean gene-based (g) markers were BLASTed against the Glycine max v.1.0 genome and the P. vulgaris v.1.0 (Andean) early release genome. In addition, gene sequences were BLASTed against the OAC Rex (Mesoamerican) genome sequence assembly. In total, fragments of 46 structural and regulatory phenylpropanoid pathway genes were characterized in this way and placed in silico on common bean and soybean sequence maps. The maps contain over 250 common bean g and SSR (simple sequence repeat) markers and identify the positions of more than 60 additional phenylpropanoid pathway gene sequences, plus the putative locations of seed coat color genes. The majority of cloned phenylpropanoid pathway gene sequences were mapped to one location in the common bean genome but had two positions in soybean. The comparison of the genomic maps confirmed previous studies, which show that common bean and soybean share genomic regions, including those containing phenylpropanoid pathway gene sequences, with conserved synteny. Indels identified in the comparison of Andean and Mesoamerican common bean 4CL gene sequences might be used to develop inter-pool phenylpropanoid pathway gene-based markers. We anticipate that the information obtained by this study will simplify and accelerate selections of common bean with specific phenylpropanoid pathway alleles to increase the contents of beneficial phenylpropanoids in common bean and other legumes.
doi:10.3389/fpls.2013.00317
PMCID: PMC3763686  PMID: 24046770
common bean; soybean; phenylpropanoid pathway; genome sequence; in silico map; comparative mapping
23.  Construction of a comparative genetic map in faba bean (Vicia faba L.); conservation of genome structure with Lens culinaris 
BMC Genomics  2008;9:380.
Background
The development of genetic markers is complex and costly in species with little pre-existing genomic information. Faba bean possesses one of the largest and least studied genomes among cultivated crop plants and no gene-based genetic maps exist. Gene-based orthologous markers allow chromosomal regions and levels of synteny to be characterised between species, reveal phylogenetic relationships and chromosomal evolution, and enable targeted identification of markers for crop breeding. In this study orthologous codominant cross-species markers have been deployed to produce the first exclusively gene-based genetic linkage map of faba bean (Vicia faba), using an F6 population developed from a cross between the lines Vf6 (equina type) and Vf27 (paucijuga type).
Results
Of 796 intron-targeted amplified polymorphic (ITAP) markers screened, 151 markers could be used to construct a comparative genetic map. Linkage analysis revealed seven major and five small linkage groups (LGs), one pair and 12 unlinked markers. Each LG was comprised of three to 30 markers and varied in length from 23.6 cM to 324.8 cM. The map spanned a total length of 1685.8 cM. A simple and direct macrosyntenic relationship between faba bean and Medicago truncatula was evident, while faba bean and lentil shared a common rearrangement relative to M. truncatula. One hundred and four of the 127 mapped markers in the 12 LGs, which were previously assigned to M. truncatula genetic and physical maps, were found in regions syntenic between the faba bean and M. truncatula genomes. However chromosomal rearrangements were observed that could explain the difference in chromosome numbers between these three legume species. These rearrangements suggested high conservation of M. truncatula chromosomes 1, 5 and 8; moderate conservation of chromosomes 2, 3, 4 and 7 and no conservation with M. truncatula chromosome 6. Multiple PCR amplicons and comparative mapping were suggestive of small-scale duplication events in faba bean. This study also provides a preliminary indication for finer scale macrosynteny between M. truncatula, lentil and faba bean. Markers originally designed from genes on the same M. truncatula BACs were found to be grouped together in corresponding syntenic areas in lentil and faba bean.
Conclusion
Despite the large size of the faba bean genome, comparative mapping did not reveal evidence for polyploidisation, segmental duplication, or significant rearrangements compared to M. truncatula, although a bias in the use of single locus markers may have limited the detection of duplications. Non-coding repetitive DNA or transposable element content provides a possible explanation for the difference in genome sizes. Similar patterns of rearrangements in faba bean and lentil compared to M. truncatula support phylogenetic studies dividing these species into the tribes Viceae and Trifoliae. However, substantial macrosynteny was apparent between faba bean and M. truncatula, with the exception of chromosome 6 where no orthologous markers were found, confirming previous investigations suggesting chromosome 6 is atypical. The composite map, anchored with orthologous markers mapped in M. truncatula, provides a central reference map for future use of genomic and genetic information in faba bean genetic analysis and breeding.
doi:10.1186/1471-2164-9-380
PMCID: PMC2533332  PMID: 18691425
24.  Diversification and Population Structure in Common Beans (Phaseolus vulgaris L.) 
PLoS ONE  2012;7(11):e49488.
Wild accessions of crops and landraces are valuable genetic resources for plant breeding and for conserving alleles and gene combinations in planta. The primary genepool of cultivated common beans includes wild accessions of Phaseolus vulgaris. These are of the same species as the domesticates and therefore are easily crossable with cultivated accessions. Molecular marker assessment of wild beans and landraces is important for the proper utilization and conservation of these important genetic resources. The goal of this research was to evaluate a collection of wild beans with fluorescent microsatellite or simple sequence repeat markers and to determine the population structure in combination with cultivated beans of all known races. Marker diversity in terms of average number of alleles per marker was high (13) for the combination of 36 markers and 104 wild genotypes that was similar to the average of 14 alleles per marker found for the 606 cultivated genotypes. Diversity in wild beans appears to be somewhat higher than in cultivated beans on a per genotype basis. Five populations or genepools were identified in structure analysis of the wild beans corresponding to segments of the geographical range, including Mesoamerican (Mexican), Guatemalan, Colombian, Ecuadorian-northern Peruvian and Andean (Argentina, Bolivia and Southern Peru). The combined analysis of wild and cultivated accessions showed that the first and last of these genepools were related to the cultivated genepools of the same names and the penultimate was found to be distinct but not ancestral to the others. The Guatemalan genepool was very novel and perhaps related to cultivars of race Guatemala, while the Colombian population was also distinct. Results suggest geographic isolation, founder effects or natural selection could have created the different semi-discrete populations of wild beans and that multiple domestications and introgression were involved in creating the diversity of cultivated beans.
doi:10.1371/journal.pone.0049488
PMCID: PMC3492280  PMID: 23145179
25.  Application of Genomic and Quantitative Genetic Tools to Identify Candidate Resistance Genes for Brown Rot Resistance in Peach 
PLoS ONE  2013;8(11):e78634.
The availability of a complete peach genome assembly and three different peach genome sequences created by our group provide new opportunities for application of genomic data and can improve the power of the classical Quantitative Trait Loci (QTL) approaches to identify candidate genes for peach disease resistance. Brown rot caused by Monilinia spp., is the most important fungal disease of stone fruits worldwide. Improved levels of peach fruit rot resistance have been identified in some cultivars and advanced selections developed in the UC Davis and USDA breeding programs. Whole genome sequencing of the Pop-DF parents lead to discovery of high-quality SNP markers for QTL genome scanning in this experimental population. Pop-DF created by crossing a brown rot moderately resistant cultivar ‘Dr. Davis’ and a brown rot resistant introgression line, ‘F8,1–42’, derived from an initial almond × peach interspecific hybrid, was evaluated for brown rot resistance in fruit of harvest maturity over three seasons. Using the SNP linkage map of Pop-DF and phenotypic data collected with inoculated fruit, a genome scan for QTL identified several SNP markers associated with brown rot resistance. Two of these QTLs were placed on linkage group 1, covering a large (physical) region on chromosome 1. The genome scan for QTL and SNP effects predicted several candidate genes associated with disease resistance responses in other host-pathogen systems. Two potential candidate genes, ppa011763m and ppa026453m, may be the genes primarily responsible for M. fructicola recognition in peach, activating both PAMP-triggered immunity (PTI) and effector-triggered immunity (ETI) responses. Our results provide a foundation for further genetic dissection, marker assisted breeding for brown rot resistance, and development of peach cultivars resistant to brown rot.
doi:10.1371/journal.pone.0078634
PMCID: PMC3823860  PMID: 24244329

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