Shoaib Ur Rehman, Jingyi Wang, Xiaoping Chang, Xueyong Zhang, Xinguo Mao, Ruilian Jing

Theoretical and Applied Genetics, April 2019, pp 1–13

Key message

We developed breeder-friendly high-throughput and cost-effective KASP marker for marker-assisted selection for grain yield related traits in wheat.

Abstract

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.

See https://link.springer.com/article/10.1007/s00122-018-3247-7

Figure 2: Gene structure and functional marker development for TaSnRK2.9-5. a Gene structure, blue blocks = untranslated region, red blocks = exon, black line = intron, M = DNA marker (100 bp). Scatter plot for KASP assays; showing clustering of accessions on the X—(FAM) and Y—(HEX) axes. Accessions colored blue have the FAM-type allele; accessions colored red have the HEX-type allele; black dots represent the NTC (non-template control). b KASP1 assay for SNP-308 nt shows allele “C” in FAM and allele “T” in HEX cluster. c KASP2 assay for SNP-1700 nt shows allele “C” in FAM and allele “A” in HEX cluster