title: Advances in genetics and molecular breeding of three legume crops of semi-arid tropics using  next-generation sequencing and high-throughput genotyping technologies.
abstract: Molecular markers are the most powerful genomic tools to increase the efficiency and precision of breeding practices for crop improvement. Progress in the development of genomic resources in the leading legume crops of the semi-arid tropics (SAT), namely, chickpea (Cicer arietinum), pigeonpea (Cajanus cajan) and groundnut (Arachis hypogaea), as compared to other crop species like cereals, has been very slow. With the advances in next-generation sequencing (NGS) and high-throughput (HTP) genotyping methods, there is a shift in development of genomic resources including molecular  markers in these crops. For instance, 2,000 to 3,000 novel simple sequence repeats (SSR) markers have been developed each  for chickpea, pigeonpea and groundnut. Based on Sanger, 454/FLX and Illumina transcript reads, transcriptome assemblies have  been developed for chickpea (44,845 transcript assembly contigs, or TACs) and pigeonpea (21,434 TACs). Illumina sequencing of some parental genotypes of mapping populations has resulted in the development of 120 million reads for chickpea and 128.9 million reads for pigeonpea. Alignment of these  Illumina reads with respective transcriptome assemblies have provided more than 10,000 SNPs each in chickpea and pigeonpea. A variety of SNP genotyping  platforms including GoldenGate, VeraCode and Competitive Allele Specific PCR (KASPar) assays have been developed in chickpea and pigeonpea. By using above resources, the first-generation or comprehensive genetic maps have been developed in  the three legume speciesmentioned above. Analysis of phenotyping data together with genotyping data has provided candidate  markers for drought-tolerance-related root traits in chickpea, resistance to foliar diseases in groundnut and sterility mosaic disease (SMD)  and fertility restoration in pigeonpea. Together with these traitassociated markers along with those already available, molecular breeding  programmes have been initiated for enhancing drought tolerance, resistance to fusarium wilt and ascochyta blight in chickpea and resistance to foliar diseases in groundnut. These trait-associated robust markers along with other genomic resources including genetic maps and genomic resources will certainly accelerate crop improvement programmes in the SAT legumes.
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics, Patancheru 502 324, India. r.k.varshney@cgiar.org
authors.forename: Rajeev K
authors.initials: RK
authors.lastname: Varshney
authors.forename: Himabindu
authors.initials: H
authors.lastname: Kudapa
authors.forename: Manish
authors.initials: M
authors.lastname: Roorkiwal
authors.forename: Mahendar
authors.initials: M
authors.lastname: Thudi
authors.forename: Manish K
authors.initials: MK
authors.lastname: Pandey
authors.forename: Rachit K
authors.initials: RK
authors.lastname: Saxena
authors.forename: Siva K
authors.initials: SK
authors.lastname: Chamarthi
authors.forename: S Murali
authors.initials: SM
authors.lastname: Mohan
authors.forename: Nalini
authors.initials: N
authors.lastname: Mallikarjuna
authors.forename: Hari
authors.initials: H
authors.lastname: Upadhyaya
authors.forename: Pooran M
authors.initials: PM
authors.lastname: Gaur
authors.forename: L
authors.initials: L
authors.lastname: Krishnamurthy
authors.forename: K B
authors.initials: KB
authors.lastname: Saxena
authors.forename: Shyam N
authors.initials: SN
authors.lastname: Nigam
authors.forename: Suresh
authors.initials: S
authors.lastname: Pande
mesh_terms: D000483:Alleles; D010367:Arachis / Q000235:genetics* / Q000276:immunology; D036561:Cajanus / Q000235:genetics* / Q000276:immunology; D002874:Chromosome Mapping; D029863:Cicer / Q000235:genetics* / Q000276:immunology; D032621:DNA Shuffling; D055864:Droughts; D020224:Expressed Sequence Tags; D059014:High-Throughput Nucleotide Sequencing; D018895:Microsatellite Repeats; D010935:Plant Diseases / Q000235:genetics* / Q000276:immunology; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D059467:Transcriptome; D014329:Tropical Climate