Development of sequence-based markers for seed protein content in pigeonpea

Molecular Genetics and Genomics : MGG
Jimmy ObalaRajeev K Varshney

Abstract

Pigeonpea is an important source of dietary protein to over a billion people globally, but genetic enhancement of seed protein content (SPC) in the crop has received limited attention for a long time. Use of genomics-assisted breeding would facilitate accelerating genetic gain for SPC. However, neither genetic markers nor genes associated with this important trait have been identified in this crop. Therefore, the present study exploited whole genome re-sequencing (WGRS) data of four pigeonpea genotypes (~ 12X coverage) to identify sequence-based markers and associated candidate genes for SPC. By combining a common variant filtering strategy on available WGRS data with knowledge of gene functions in relation to SPC, 108 sequence variants from 57 genes were identified. These genes were assigned to 19 GO molecular function categories with 56% belonging to only two categories. Furthermore, Sanger sequencing confirmed presence of 75.4% of the variants in 37 genes. Out of 30 sequence variants converted into CAPS/dCAPS markers, 17 showed high level of polymorphism between low and high SPC genotypes. Assay of 16 of the polymorphic CAPS/dCAPS markers on an F2 population of the cross ICP 5529 (high SPC) × ICP 11605 (low SPC), resulted in...Continue Reading

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Citations

Feb 18, 2020·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Abhishek BohraRachit K Saxena
Dec 18, 2019·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Rachit K SaxenaRajeev K Varshney
Oct 21, 2020·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Rachit K SaxenaRajeev K Varshney
May 6, 2021·The Plant Genome·Lekha T PazhamalaRajeev K Varshney

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Methods Mentioned

BETA
PCR
genotyping

Software Mentioned

Excel
IndelRealigner analysis toolkit ( GATK )
BLISTER
DNA Baser
GAB
Primer3Plus
DNA Baser Sequence Assembler
snpEff
dCAPS Finder
Bowtie

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