Abstract
Key messageWe developed breeder-friendly high-throughput and cost-effective KASP marker for marker-assisted selection for grain yield related traits in wheat.Plant-specific protein kinase, SnRK2s, is a major family of signaling genes associated with metabolic regulations, nutrient utilization and response to external stimuli. In the present study, three copies of TaSnRK2.9 were isolated from chromosomes 5A, 5B and 5D of wheat (Triticum aestivum L.). The coding regions of TaSnRK2.9-5A, TaSnRK2.9-5B and promoter region of TaSnRK2.9-5D were investigated for sequence polymorphism. Single nucleotide polymorphisms (SNPs) were identified for TaSnRK2.9-5A, while no polymorphism was identified in TaSnRK2.9-5B and TaSnRK2.9-5D. The nucleotide sequence of TaSnRK2.9-5A consisted of 2180 bp having eight introns and nine exons. Three SNPs were identified at 308 nt, 698 nt and 1700 nt. For high-throughput genotyping, two kompetitive allele-specific PCR (KASP) markers were developed. Four haplotypes Hap-5A-1, Hap-5A-2, Hap-5A-3 and Hap-5A-4 were detected in wheat populations collected from China, Europe and Pakistan. Association analysis was performed with mixed linear model in TASSEL (v 5.0). The results indicated that Hap-5A-1/2 of TaSnRK2.9-5A were significantly associated with high thousand kernel weight, while Hap-5A-4 with high grains per spike. Overexpressing transgenic rice also showed higher grains per spike which is in accordance with association analysis results. Geographic distribution and allelic frequency indicted that the favored haplotypes were positively selected in Chinese (Hap-5A-1/2), Pakistani (Hap-5A-1), east European (Hap-5A-1) and west European (Hap-5A-4) wheat breeding. The results suggest that the developed KASP markers can be utilized in yield improvement by marker-assisted selection in wheat breeding.
Highlights
Crop productivity is limited by diverse climatic fluctuations including drought, extreme temperatures, and water logging
The Single nucleotide polymorphisms (SNPs) at 1700 nt (A/C) in exon led to an amino acid change (CAG → Gln to CCG → Pro) without changing protein 3D structure (Supplementary Fig. 1)
KASP1 was developed for SNP at 308 nt, whereas KASP2 was developed for SNP at 1700 nt (Fig. 2b, c)
Summary
Crop productivity is limited by diverse climatic fluctuations including drought, extreme temperatures (cold and heat), and water logging. Breeding for stress resilient crop varieties is vital to sustain productivity of food commodities. A comprehensive understanding of gene networks underlying important adaptive traits showing resilience to weather extremes would benefit breeding for new cultivars (Mickelbart et al 2015). Common wheat (Triticum aestivum L.) is the staple food of more than 4.5 billion people in 94 developing countries (Braun et al 2010), and doubling the wheat production by 2050 due to population surge in the face of climate change and continuously declining arable land is a big challenge (Li et al 2018). Breeding for high grain yield is the utmost objective and there is continuous search for genes underpinning yield and its direct contributing traits
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