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Leveraging barrel medic genome sequence for the development and use of genomic resources for genetic analysis and breeding in legumes
Bi, Rabiya; Chandappa, Lohithaswa H; Siddalingaiah, Lokesh; Kenchanmane Raju, Sunil Kumar; Hassan Balakrishna, Shilpa; Kumar, Jyothi; Kuruba, Vinutha; Hittalmani, Shailaja.
  • Bi, Rabiya; College of Agriculture. Department of Genetics and Plant Breeding. IN
  • Chandappa, Lohithaswa H; College of Agriculture. Department of Genetics and Plant Breeding. IN
  • Siddalingaiah, Lokesh; University of Mysore. Department of Applied Botany and Biotechnology. IN
  • Kenchanmane Raju, Sunil Kumar; University of Agricultural Sciences. College of Agriculture. Department of Genetics and Plant Breeding. IN
  • Hassan Balakrishna, Shilpa; University of Agricultural Sciences. College of Agriculture. Department of Genetics and Plant Breeding. IN
  • Kumar, Jyothi; University of Agricultural Sciences. College of Agriculture. Department of Genetics and Plant Breeding. IN
  • Kuruba, Vinutha; University of Mysore. Department of Applied Botany and Biotechnology. IN
  • Hittalmani, Shailaja; University of Agricultural Sciences. College of Agriculture. Department of Genetics and Plant Breeding. IN
Electron. j. biotechnol ; 39: 30-41, may. 2019. tab, ilus
Article in English | LILACS | ID: biblio-1051590
ABSTRACT

BACKGROUND:

A total of 62,591 cowpea expressed sequence tags (ESTs) were BLAST aligned to the whole-genome sequence of barrel medic (Medicago truncatula) to develop conserved intron scanning primers (CISPs). The efficacy of the primers was tested across 10 different legumes and on different varieties of cowpea, chickpea, and pigeon pea. Genetic diversity was assessed using the same primers on different cowpea genotypes. Singlenucleotide polymorphisms (SNPs) were detected, which were later converted to length polymorphism markers for easy genotyping. CISPs developed in this study were used in tagging resistance to bacterial leaf blight disease in cowpea.

RESULTS:

A total of 1262 CISPs were designed. The single-copy amplification success rates using these primers on 10 different legumes and on different varieties of cowpea, chickpea, and pigeon pea were approximately 60% in most of the legumes except soybean (47%) and peanut (37%). Genetic diversity analysis of 35 cowpea genotypes using 179 CISPs revealed 123 polymorphic markers with PIC values ranging from 0.05 to 0.59. Potential SNPs identified in cowpea, chickpea, and pigeon pea were converted to PCR primers of various sizes for easy genotyping. Using the markers developed in this study, a genetic linkage map was constructed with 11 linkage groups in cowpea. QTL mapping with 194 F3 progeny families derived from the cross C-152 × V-16 resulted in the identification of three QTLs for resistance to bacterial leaf blight disease.

Conclusions:

CISPs were proved to be efficient markers to identify various other marker classes like SNPs through comparative genomic studies in lesser studied crops and to aid in systematic sampling of the entire genome for well-distributed markers at low cost
Subject(s)


Full text: Available Index: LILACS (Americas) Main subject: Genome, Plant / Genomics / Medicago truncatula Language: English Journal: Electron. j. biotechnol Journal subject: Biotechnology Year: 2019 Type: Article Affiliation country: India Institution/Affiliation country: College of Agriculture/IN / University of Agricultural Sciences/IN / University of Mysore/IN

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Full text: Available Index: LILACS (Americas) Main subject: Genome, Plant / Genomics / Medicago truncatula Language: English Journal: Electron. j. biotechnol Journal subject: Biotechnology Year: 2019 Type: Article Affiliation country: India Institution/Affiliation country: College of Agriculture/IN / University of Agricultural Sciences/IN / University of Mysore/IN