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

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Relation http://oar.icrisat.org/6163/
http://dx.doi.org/10.1007/s12038-012-9228-0
 
Title Advances in genetics and molecular breeding of three legume crops of semi-arid tropics using next-generation sequencing and high-throughput genotyping technologies
 
Creator Varshney, R K
Kudapa, H
Roorkiwal, M
Thudi, M
Pandey, M K
Saxena, R K
Chamarthi, S K
Murali Mohan, S
Mallikarjuna, N
Upadhyaya, H D
Gaur, P M
Krishnamurthy, L
Saxena, K B
Nigam, S N
Pande, S
 
Subject Chickpea
Pigeonpea
Groundnut
Genetics and Genomics
Agriculture-Farming, Production, Technology, Economics
 
Description 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 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 legume
 
Publisher Indian Academy of Sciences
 
Date 2012
 
Type Article
PeerReviewed
 
Format application/pdf
 
Language en
 
Rights —
 
Identifier http://oar.icrisat.org/6163/1/2012_JB_legumes.pdf
Varshney, R K and Kudapa, H and Roorkiwal, M and Thudi, M and Pandey, M K and Saxena, R K and Chamarthi, S K and Murali Mohan, S and Mallikarjuna, N and Upadhyaya, H D and Gaur, P M and Krishnamurthy, L and Saxena, K B and Nigam, S N 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. Journal of Biosciences, 37 (5). pp. 811-820. ISSN 0973-7138