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Pre-harvest sprouting (PHS) resistance is one of the most important traits in wheat breeding. Characterization of Viviparous-1 (Vp-1) haplotypes in wheat related species will further our understanding of the role of Vp-1 in PHS resistance of bread wheats. The present paper reported Vp-1 haplotype analyzes of 77 accessions of wheat related species including T. monococcum and T. boeoticum (AmAm), T. durum (AABB), T. dicoccoides (AABB) and Ae. tauschii (DD). A total of 11 novel Vp-1 haplotypes were identified in these species including three in T. monococcum which were designated as TmVp-1A1, TmVp-1A2, TmVp-1A3, three in T. boeoticum, designated as TbVp-1A1, TbVp-1A2 and TbVp-1A3, two in T. durum, designated as TduVp-1B1 and TduVp-1B2, and three in Ae. tauschii designated as AetVp-1D1, AetVp-1D2 and AetVp-1D3, respectively. Among these haplotypes explored, TduVp-1B1 was identical to TaVp-1Be which was detected in a PHS resistant Chinese landrace. Semi-quantitative RT-PCR analysis demonstrated that the presence of alternatively spliced transcripts of the Vp-1 homologues in these wheat related species. The level of correctly spliced transcripts varies among the haplotypes, and was correlated with the degree of ABA responsiveness during seed germination. It appeared that Vp-1 mis-splicing and some indel variations in bread wheats originated from its progenitors and were retained during polyploidization. Moreover, haplotypes with better Vp-1 splicing such as TbVp-1A2 of T. boeoticum and TduVp-1B1 of T. durum species might be valuable in breeding PHS tolerant wheat.

Since the discovery of acrylamide in food, and the identification of free asparagine as the key determinant of acrylamide concentration in wheat products, our understanding of how grain asparagine content is regulated has improved greatly. However, the targeted reduction in grain asparagine content has not been widely implemented in breeding programmes so far. Here we summarise how free asparagine concentration relates to other quality and agronomic traits and show that these relationships are unlikely to pose major issues for the breeding of low-asparagine wheat. We also outline the strategies that are possible for the breeding of low-asparagine wheat, using both natural and induced variation.

Background Pre-harvest sprouting (PHS) of wheat grain leads to a reduction in grain yield and quality. The availability of markers for marker-assisted selection (MAS) of PHS resistance will serve to enhance breeding selection and advancement of lines for cultivar development. The aim of this study was to identify candidate regions and develop molecular markers for PHS resistance in wheat. This was achieved via high density mapping of single nucleotide polymorphism (SNP) markers from an Illumina 90 K Infinium Custom Beadchip in a doubled haploid (DH) population derived from a RL4452/‘AC Domain’ cross and subsequent detection of quantitative trait loci (QTL) for PHS related traits (falling number [FN], germination index [GI] and sprouting index [SI]). SNP marker sequences flanking QTL were used to locate colinear regions in Brachypodium and rice, and identify genic markers associated with PHS resistance that can be utilized for MAS in wheat. Results A linkage map spanning 2569.4 cM was constructed with a total of 12,201 SNP, simple sequence repeat (SSR), diversity arrays technology (DArT) and expressed sequence tag (EST) markers. QTL analyses using Multiple Interval Mapping (MIM) identified four QTL for PHS resistance traits on chromosomes 3B, 4A, 7B and 7D. Sequences of SNPs flanking these QTL were subject to a BLASTN search on the International Wheat Genome Sequencing Consortium (IWGSC) database (http://wheat-urgi.versailles.inra.fr/Seq-Repository). Best survey sequence hits were subject to a BLASTN search on Gramene (www.gramene.org) against both Brachypodium and rice databases, and candidate genes and regions for PHS resistance were identified. A total of 18 SNP flanking sequences on chromosomes 3B, 4A, 7B and 7D were converted to KASP markers and validated with matching genotype calls of Infinium SNP data. Conclusions Our study identified candidate genes involved in abscissic acid (ABA) and gibberellin (GA) metabolism, and flowering time in four genomic regions of Brachypodium and rice respectively, in addition to 18 KASP markers for PHS resistance in wheat. These markers can be deployed in future genetic studies of PHS resistance and might also be useful in the evaluation of PHS in germplasm and breeding material. Electronic supplementary material The online version of this article (doi:10.1186/s12870-014-0340-1) contains supplementary material, which is available to authorized users.