Advances in genetics and molecular breeding of three legume crops of semi-arid tropics using next-generation sequencing and high-throughput genotyping technologies uri icon

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 > 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 species mentioned 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 trait-associated 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.
  • Molecular markers are the most powerful genomic tools to increase the efficiency and precision of breeding practicesfor crop improvement. Progress in the development of genomic resources in the leading legume crops of the semi-aridtropics (SAT), namely, chickpea (Cicer arietinum), pigeonpea (Cajanus cajan) and groundnut (Arachis hypogaea), ascompared 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 resourcesincluding 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 andIllumina transcript reads, transcriptome assemblies have been developed for chickpea (44,845 transcriptassembly contigs, or TACs) and pigeonpea (21,434 TACs). Illumina sequencing of some parental genotypesof mapping populations has resulted in the development of 120 million reads for chickpea and 128.9 millionreads for pigeonpea. Alignment of these Illumina reads with respective transcriptome assemblies haveprovided >10,000 SNPs each in chickpea and pigeonpea. A variety of SNP genotyping platforms includingGoldenGate, VeraCode and Competitive Allele Specific PCR (KASPar) assays have been developed inchickpea and pigeonpea. By using above resources, the first-generation or comprehensive genetic maps havebeen developed in the three legume speciesmentioned above. Analysis of phenotyping data together with genotyping datahas provided candidate markers for drought-tolerance-related root traits in chickpea, resistance to foliar diseases ingroundnut and sterility mosaic disease (SMD) and fertility restoration in pigeonpea. Together with these traitassociatedmarkers along with those already available, molecular breeding programmes have been initiated forenhancing drought tolerance, resistance to fusarium wilt and ascochyta blight in chickpea and resistance tofoliar diseases in groundnut. These trait-associated robust markers along with other genomic resources includinggenetic maps and genomic resources will certainly accelerate crop improvement programmes in the SAT legume
  • [Varshney RK, Kudapa H, Roorkiwal M, Thudi M, Pandey MK, Saxena RK, Chamarthi SK, Mohan SM, Mallikarjuna N, Upadhyaya H, Gaur PM, Krishnamurthy L, Saxena KB, Nigam SN and Pande S 2012 Advances in genetics and molecular breeding of three legume crops of semi-arid tropics using next-generation sequencing and high-throughput genotyping technologies. J. Biosci. 37 811-820] DOI 10.1007/s12038-012-9228-0

publication date

  • 2012
  • 2012
  • 2012