Characterization of the rich haplotypes of Viviparous-1A in Chinese wheats and development of a novel sequence-tagged site marker for pre-harvest sprouting resistance

Pre-harvest sprouting (PHS) reduces the quality of wheat (Triticum aestivum L.) and the economic value of the grain. Our previous studies characterized the haplotypes of Viviparous-1B (Vp-1B) and its association with PHS resistance in Chinese wheats. The objective of this study was to analyze the haplotypes of Viviparous-1A (Vp-1A) and Viviparous-1D (Vp-1D) in a collection of 103 widely-grown winter wheats in China, and their associations with PHS resistance. In total, 17 Vp-1A haplotypes were explored on chromosome 3A of bread wheat, and were located in three major regions, the third intron, fifth intron and sixth exon, and designated TaVp-1Aam, TaVp-1Aan, TaVp-1Aao, TaVp-1Abm, TaVp-1Abn, TaVp-1Agm, TaVp-1Ahm, TaVp-1Ahn, TaVp-1Aho, TaVp-1Aim, TaVp-1Ain, TaVp-1Aio, TaVp-1Ajm, TaVp-1Ajn, TaVp-1Akm, TaVp-1Alm and TaVp-1Aln, respectively. However, no allelic variation of Vp-1D was found in this set of germplasm. Based on the haplotypes explored and their average germination index values, a novel co-dominant sequence-tagged site marker of the TaVp-1A gene was developed and designated Vp1A3. In most cases, haplotype TaVp-1Agm was associated with higher resistance to PHS. By combining with our previously exploited Vp1B3 marker, the efficiency of marker-assisted selection for PHS-resistant varieties was improved. Moreover, while the haplotype combination of TaVp-1Aam and TaVp-1Ba was associated with greater PHS susceptibility, the haplotype combinations TaVp-1Agm and TaVp-1Bb, TaVp-1Agm and TaVp-1Ba, TaVp-1Aim and TaVp-1Bb, and TaVp-1Aam and TaVp-1Bb could confer higher PHS resistance and be used as potential parental lines for molecular marker-assisted wheat breeding for PHS resistance.