Browsing by Author "Ajay K. Mahato"

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Allelic sequence variation in the Sub1A, Sub1B and Sub1C genes among diverse rice cultivars and its association with submergence tolerance
(Nature Research, 2020) Anuradha Singh; Yashi Singh; Ajay K. Mahato; Pawan K. Jayaswal; Sangeeta Singh; Renu Singh; Neera Yadav; A.K. Singh; P.K. Singh; Rakesh Singh; Rajesh Kumar; Endang M. Septiningsih; H.S. Balyan; Nagendra K. Singh; Vandna Rai
Erratic rainfall leading to flash flooding causes huge yield losses in lowland rice. The traditional varieties and landraces of rice possess variable levels of tolerance to submergence stress, but gene discovery and utilization of these resources has been limited to the Sub1A-1 allele from variety FR13A. Therefore, we analysed the allelic sequence variation in three Sub1 genes in a panel of 179 rice genotypes and its association with submergence tolerance. Population structure and diversity analysis based on a 36-plex genome wide genic-SNP assay grouped these genotypes into two major categories representing Indica and Japonica cultivar groups with further sub-groupings into Indica, Aus, Deepwater and Aromatic-Japonica cultivars. Targetted re-sequencing of the Sub1A, Sub1B and Sub1C genes identfied 7, 7 and 38 SNPs making 8, 9 and 67 SNP haplotypes, respectively. Haplotype networks and phylogenic analysis revealed evolution of Sub1B and Sub1A genes by tandem duplication and divergence of the ancestral Sub1C gene in that order. The alleles of Sub1 genes in tolerant reference variety FR13A seem to have evolved most recently. However, no consistent association could be found between the Sub1 allelic variation and submergence tolerance probably due to low minor allele frequencies and presence of exceptions to the known Sub1A-1 association in the genotype panel. We identified 18 cultivars with non-Sub1A-1 source of submergence tolerance which after further mapping and validation in bi-parental populations will be useful for development of superior flood tolerant rice cultivars. © 2020, The Author(s).
The first draft of the pigeonpea genome sequence
(2012) Nagendra K. Singh; Deepak K. Gupta; Pawan K. Jayaswal; Ajay K. Mahato; Sutapa Dutta; Sangeeta Singh; Shefali Bhutani; Vivek Dogra; Bikram P. Singh; Giriraj Kumawat; Jitendra K. Pal; Awadhesh Pandit; Archana Singh; Hukum Rawal; Akhilesh Kumar; G. Rama Prashat; Ambika Khare; Rekha Yadav; Ranjit S. Raje; Mahendra N. Singh; Subhojit Datta; Bashasab Fakrudin; Keshav B. Wanjari; Rekha Kansal; Prasanta K. Dash; Pradeep K. Jain; Ramcharan Bhattacharya; Kishor Gaikwad; Trilochan Mohapatra; R. Srinivasan; Tilak R. Sharma
Pigeonpea (Cajanus cajan) is an important grain legume of the Indian subcontinent, South-East Asia and East Africa. More than eighty five percent of the world pigeonpea is produced and consumed in India where it is a key crop for food and nutritional security of the people. Here we present the first draft of the genome sequence of a popular pigeonpea variety 'Asha'. The genome was assembled using long sequence reads of 454 GS-FLX sequencing chemistry with mean read lengths of >550 bp and >10-fold genome coverage, resulting in 510,809,477 bp of high quality sequence. Total 47,004 protein coding genes and 12,511 transposable elements related genes were predicted. We identified 1,213 disease resistance/defense response genes and 152 abiotic stress tolerance genes in the pigeonpea genome that make it a hardy crop. In comparison to soybean, pigeonpea has relatively fewer number of genes for lipid biosynthesis and larger number of genes for cellulose synthesis. The sequence contigs were arranged in to 59,681 scaffolds, which were anchored to eleven chromosomes of pigeonpea with 347 genic-SNP markers of an intra-species reference genetic map. Eleven pigeonpea chromosomes showed low but significant synteny with the twenty chromosomes of soybean. The genome sequence was used to identify large number of hypervariable 'Arhar' simple sequence repeat (HASSR) markers, 437 of which were experimentally validated for PCR amplification and high rate of polymorphism among pigeonpea varieties. These markers will be useful for fingerprinting and diversity analysis of pigeonpea germplasm and molecular breeding applications. This is the first plant genome sequence completed entirely through a network of Indian institutions led by the Indian Council of Agricultural Research and provides a valuable resource for the pigeonpea variety improvement. © 2011 Society for Plant Biochemistry and Biotechnology.