Genome-Wide Association Study for Grain Protein, Thousand Kernel Weight, and Normalized Difference Vegetation Index in Bread Wheat (Triticum aestivum L.)

Gopalareddy Krishnappa; Hanif Khan; Hari Krishna; Narayana Bhat Devate; Satish Kumar; Chandra Nath Mishra; Om Parkash; Sachin Kumar; Monu Kumar; Harohalli Masthigowda Mamrutha; Gyanendra Pratap Singh; Gyanendra Singh

doi:10.3390/genes14030637

Genome-Wide Association Study for Grain Protein, Thousand Kernel Weight, and Normalized Difference Vegetation Index in Bread Wheat (Triticum aestivum L.)

Genes (Basel). 2023 Mar 3;14(3):637. doi: 10.3390/genes14030637.

Authors

Affiliations

¹ ICAR-Indian Institute of Wheat and Barley Research, Karnal 132001, India.
² ICAR-Sugarcane Breeding Institute, Coimbatore 641007, India.
³ ICAR-Indian Agricultural Research Institute, New Delhi 110012, India.
⁴ ICAR-Indian Agricultural Research Institute, Gauria Karma 825411, India.
⁵ ICAR-National Bureau of Plant Genetic Resources, New Delhi 110012, India.

Abstract

Genomic regions governing grain protein content (GPC), 1000 kernel weight (TKW), and normalized difference vegetation index (NDVI) were studied in a set of 280 bread wheat genotypes. The genome-wide association (GWAS) panel was genotyped using a 35K Axiom array and phenotyped in three environments. A total of 26 marker-trait associations (MTAs) were detected on 18 chromosomes covering the A, B, and D subgenomes of bread wheat. The GPC showed the maximum MTAs (16), followed by NDVI (6), and TKW (4). A maximum of 10 MTAs was located on the B subgenome, whereas, 8 MTAs each were mapped on the A and D subgenomes. In silico analysis suggest that the SNPs were located on important putative candidate genes such as NAC domain superfamily, zinc finger RING-H2-type, aspartic peptidase domain, folylpolyglutamate synthase, serine/threonine-protein kinase LRK10, pentatricopeptide repeat, protein kinase-like domain superfamily, cytochrome P450, and expansin. These candidate genes were found to have different roles including regulation of stress tolerance, nutrient remobilization, protein accumulation, nitrogen utilization, photosynthesis, grain filling, mitochondrial function, and kernel development. The effects of newly identified MTAs will be validated in different genetic backgrounds for further utilization in marker-aided breeding.

Keywords: GPC; GWAS; NDVI; candidate genes; wheat.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Bread
Genome-Wide Association Study*
Grain Proteins*
Plant Breeding
Protein Kinases
Triticum / genetics

Substances

Grain Proteins
Protein Kinases

Grants and funding

This study was supported with funding provided by the Indian Council of Agricultural Research (ICAR) and Bill Melinda Gate Foundation (BMGF) under the project Application of next-generation breeding, genotyping and digitalization approaches for improving the genetic gain in Indian staple crops. ICAR-BMGF (Grant number # OPP1194767).