An integrated physical, genetic and cytogenetic map around the sunn locus of Medicago truncatula

The sunn mutation of Medicago truncatula is a single-gene mutation that confers a novel supernodulation phenotype in response to inoculation with Sinorhizobium meliloti. We took advantage of the publicly available codominant PCR markers, the high-density genetic map, and a linked cytogenetic map to define the physical and genetic region containing sunn. We determined that sunn is located at the bottom of linkage group 4, where a fine-structure genetic map was used to place the locus within a similar to400-kb contig of bacterial artificial chromosome (BAC) clones. Genetic analyses of the sunn contig, as well as of a second, closely linked BAC contig designated NUM1, indicate that the physical to genetic distance within this chromosome region is in the range of 1000 -1100 kb.cM(-1). The ratio of genetic to cytogenetic distance determined across the entire region is 0.3 cM-mum(-1). These estimates are in good agreement with the empirically determined value of similar to300 kb-mum(-1) measured for the NUM1 contig. The assignment of sunn to a defined physical interval should provide a basis for sequencing and ultimately cloning the responsible gene

The Quantitative Genetics of Flowering Traits in Wide Crosses of Chickpea

Chickpea (Cicer arietinum L.) is one of the most ımportant food legume crops in the world. Chickpea is valued for its nutritive seed composition, which is high in protein content and used increasingly as a substitute for animal protein. Days to fırst flowerıng is an important component of the adaptation and productivity of chickpea in rainfed environments characterized by terminal drought and heat stress. This study aimed to identify the inheritance pattern and identify quantitative trait loci (QTLs) for days to first flowering and flowering color in F2:4 generation nested association mapping (NAM) populations of chickpea obtained using wide crosses between Gokce as the cultivated variety and wild accessions of C. reticulatum and C. echinospermum. A total of ten populations of 113 to 191 individuals each were grown under field conditions near Sanliurfa, Turkey. Two populations were genotyped for 46 single nucleotide polymorphism (SNP) markers, enabling QTL analysis. Flowering time differed between families, with the frequency distributions indicating quantitative inheritance controlled by both genes of major and minor effects. Three significant QTLs for the flowering time were mapped in one mapping family. For flower color, chi-square tests showed that five populations accepted single-gene action, two populations accepted two-gene action, and three populations accepted neither model. Two significant QTLs at three genomic regions were identified across the two genotyped populations. Days to first flowering was positively correlated with flower color for two of the ten populations. The diversity of QTLs identified underscored the potential of crop wild relatives of chickpea as sources of novel alleles for chickpea breeding

Large scale development of BAC-end associated SSR markers in Pigeonpea [Cajanus cajan (L.) Millspaugh]

Low levels of polymorphism and lack of sufficient numbers of microsatellite markers are factors that constrain molecular breeding in pigeonpea. BAC-end sequencing approach was used to obtain a set of BAC-associated SSRs (simple sequence repeats), providing a resource for both genetic and physical map analysis. 87,590 pigeonpea BAC end sequences, representing 56.5 Mb from genome, were surveyed for the presence of microsatellite using MIcroSAtellite (MISA). Among 18,149 pigeonpea microsatellites (1 SSR per 32.1Mbp) di-nucleotide motifs were the most abundant (41%), followed by tri-nucleotide motifs (~10%). Most di- and tri-nucleotide sequences were AT-rich (i.e., TA and TAA). With the goal of increasing genetic marker density, 6,590 oligonucleotide primers pairs were designed, 3,072 primer pairs were synthesized and tested. Amplified products were obtained for 2,946 primer pairs and were used to identify polymorphism in a set of 24 pigeonpea genotypes that are parents of different mapping populations segregating for Fusarium wilt (FW), sterility mosaic (SM) and water logging. Number of polymorphic markers identified ranged from 100-415 across different crosses. Genotyping of these polymorphic markers in the respective mapping populations is underway. Marker genotyping data along with phenotyping data obtained from these mapping populations will facilitate mapping of QTLs/genes for the traits of interest to breeder

Novel SSR markers from BAC-End Sequences, DArT Arrays and a comprehensive genetic map with 1,291 marker loci for Chickpea (Cicer arietinum L.)

Chickpea (Cicer arietinum L.) is the third most important cool season food legume, cultivated in arid and semi-arid regions of the world. The goal of this study was to develop novel molecular markers such as microsatellite or simple sequence repeat (SSR) markers from bacterial artificial chromosome (BAC)-end sequences (BESs) and diversity arrays technology (DArT) markers, and to construct a high-density genetic map based on recombinant inbred line (RIL) population ICC 4958 (C. arietinum)×PI 489777 (C. reticulatum). A BAC-library comprising 55,680 clones was constructed and 46,270 BESs were generated. Mining of these BESs provided 6,845 SSRs, and primer pairs were designed for 1,344 SSRs. In parallel, DArT arrays with ca. 15,000 clones were developed, and 5,397 clones were found polymorphic among 94 genotypes tested. Screening of newly developed BES-SSR markers and DArT arrays on the parental genotypes of the RIL mapping population showed polymorphism with 253 BES-SSR markers and 675 DArT markers. Segregation data obtained for these polymorphic markers and 494 markers data compiled from published reports or collaborators were used for constructing the genetic map. As a result, a comprehensive genetic map comprising 1,291 markers on eight linkage groups (LGs) spanning a total of 845.56 cM distance was developed (http://cmap.icrisat.ac.in/cmap/sm/cp/thudi/). The number of markers per linkage group ranged from 68 (LG 8) to 218 (LG 3) with an average inter-marker distance of 0.65 cM. While the developed resource of molecular markers will be useful for genetic diversity, genetic mapping and molecular breeding applications, the comprehensive genetic map with integrated BES-SSR markers will facilitate its anchoring to the physical map (under construction) to accelerate map-based cloning of genes in chickpea and comparative genome evolution studies in legumes

Large‐scale development of cost‐effective SNP marker assays for diversity assessment and genetic mapping in chickpea and comparative mapping in legumes

A set of 2486 single nucleotide polymorphisms (SNPs) were compiled in chickpea using four approaches, namely (i) Solexa/Illumina sequencing (1409), (ii) amplicon sequencing of tentative orthologous genes (TOGs) (604), (iii) mining of expressed sequence tags (ESTs) (286) and (iv) sequencing of candidate genes (187). Conversion of these SNPs to the cost-effective and flexible throughput Competitive Allele Specific PCR (KASPar) assays generated successful assays for 2005 SNPs. These marker assays have been designated as Chickpea KASPar Assay Markers (CKAMs). Screening of 70 genotypes including 58 diverse chickpea accessions and 12 BC3F2 lines showed 1341 CKAMs as being polymorphic. Genetic analysis of these data clustered chickpea accessions based on geographical origin. Genotyping data generated for 671 CKAMs on the reference mapping population (Cicer arietinum ICC 4958 × Cicer reticulatum PI 489777) were compiled with 317 unpublished TOG-SNPs and 396 published markers for developing the genetic map. As a result, a second-generation genetic map comprising 1328 marker loci including novel 625 CKAMs, 314 TOG-SNPs and 389 published marker loci with an average inter-marker distance of 0.59 cM was constructed. Detailed analyses of 1064 mapped loci of this second-generation chickpea genetic map showed a higher degree of synteny with genome of Medicago truncatula, followed by Glycine max, Lotus japonicus and least with Vigna unguiculata. Development of these cost-effective CKAMs for SNP genotyping will be useful not only for genetics research and breeding applications in chickpea, but also for utilizing genome information from other sequenced or model legumes

Whole-genome resequencing of 292 pigeonpea accessions identifies genomic regions associated with domestication and agronomic traits

Pigeonpea (Cajanus cajan), a tropical grain legume with low input requirements, is expected to continue to have an important role in supplying food and nutritional security in developing countries in Asia, Africa and the tropical Americas. From whole-genome resequencing of 292 Cajanus accessions encompassing breeding lines, landraces and wild species, we characterize genome-wide variation. On the basis of a scan for selective sweeps, we find several genomic regions that were likely targets of domestication and breeding. Using genome-wide association analysis, we identify associations between several candidate genes and agronomically important traits. Candidate genes for these traits in pigeonpea have sequence similarity to genes functionally characterized in other plants for flowering time control, seed development and pod dehiscence. Our findings will allow acceleration of genetic gains for key traits to improve yield and sustainability in pigeonpea

Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement

Chickpea (Cicer arietinum) is the second most widely grown legume crop after soybean, accounting for a substantial proportion of human dietary nitrogen intake and playing a crucial role in food security in developing countries. We report the ∼738-Mb draft whole genome shotgun sequence of CDC Frontier, a kabuli chickpea variety, which contains an estimated 28,269 genes. Resequencing and analysis of 90 cultivated and wild genotypes from ten countries identifies targets of both breeding-associated genetic sweeps and breeding-associated balancing selection. Candidate genes for disease resistance and agronomic traits are highlighted, including traits that distinguish the two main market classes of cultivated chickpea—desi and kabuli. These data comprise a resource for chickpea improvement through molecular breeding and provide insights into both genome diversity and domestication

Resequencing of 429 chickpea accessions from 45 countries provides insights into genome diversity, domestication and agronomic traits

We report a map of 4.97 million single-nucleotide polymorphisms of the chickpea from whole-genome resequencing of 429 lines sampled from 45 countries. We identified 122 candidate regions with 204 genes under selection during chickpea breeding. Our data suggest the Eastern Mediterranean as the primary center of origin and migration route of chickpea from the Mediterranean/Fertile Crescent to Central Asia, and probably in parallel from Central Asia to East Africa (Ethiopia) and South Asia (India). Genome-wide association studies identified 262 markers and several candidate genes for 13 traits. Our study establishes a foundation for large-scale characterization of germplasm and population genomics, and a resource for trait dissection, accelerating genetic gains in future chickpea breeding

Cytokinin accumulation and an altered ethylene response mediate the pleiotropic phenotype of the pea nodulation mutant R50 (sym16)

R50 (sym16), a pleiotropic mutant of Pisum sativum L., is short, has thickened internodes and roots, and has a reduced number of lateral roots and nodules. Its low nodule phenotype can be restored with the application of ethylene inhibitors; furthermore, it can be mimicked by applying cytokinins (CKs) to the roots of the parent line 'Sparkle'. Here, we report on the etiolation phenotypes of R50 and 'Sparkle', and on the interactive roles of ethylene and CKs in these lines. R50 displayed an altered etiolation phenotype, as it was shorter and thicker, and had more developed leaves than dark-grown 'Sparkle'. Shoot morphological differences induced by exogenous ethylene or CKs were found to be less severe for R50. Ethylene inhibitor application induced root and shoot elongation and encouraged apical hook opening in both etiolated lines. Liquid chromatography - tandem mass spectrometry analysis indicated that CK concentrations in R50 were higher than in 'Sparkle', particularly in mature shoots where the levels were maintained at elevated concentrations. These differences indicate a reduction in the CK catabolism of R50. The accumulation of CKs can be directly related to several traits of R50, with the reduced number of nodules and altered shoot ethylene response being likely indirect effects