Identification of candidate genes, regions and markers for pre-harvest sprouting resistance in wheat (Triticum aestivum L.)

Abstract

BackgroundPre-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.ResultsA 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.ConclusionsOur 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 materialThe online version of this article (doi:10.1186/s12870-014-0340-1) contains supplementary material, which is available to authorized users.

Map-Based Cloning of qSD1-2 Identified a Gibberellin Synthesis Gene Regulating the Development of Endosperm-Imposed Dormancy in Rice

“…Natural mutants used to develop semidwarf varieties in the barley (Hordeum vulgare), sorghum (Sorghum bicolor), and wheat crops usually have a mild negative effect on plant development, and some of them are GA sensitive (Gale and Marshall, 1975;Franckowiak and Pecio, 1992;Rodríguez et al, 2012). Some seed dormancy QTLs in barley and wheat have been associated with GA metabolism genes by comparative genomics research using rice as the reference (Li et al, 2004;Cabral et al, 2014). Thus, the information from this research would encourage exploring new functions of GA mutants to enrich knowledge on seed development and to test if orthologous genes are involved in the regulation of seed dormancy in different species.…”

Inheritance patterns of the response to in vitro doubled haploid induction in perennial ryegrass (Lolium perenne L.)

“…An insignificant association of embryo production with plant regeneration, invaluable for the creation of mapping populations for genetic and genomic studies (Forster et al 2007) and the simplification of genome sequence assembly (Dunwell 2010). Through self-pollination, DH populations can be propagated indefinitely and stored as seed, thus allowing for multi-year and multi-location phenotyping for QTL discovery (Guo et al 2013), which has been particularly useful in cereal species (Cabral et al 2014;Sannemann et al 2015;Obsa et al 2016). In breeding programs, DH production replaces inbred line development through repeated self-pollination, so that major reductions in the time to cultivar release are achieved (Dwivedi et al 2015).…”

Seed dormancy QTL identification across a Sorghum bicolor segregating population

“…Sorghum qGI-3 location was directly carried out using the available syntenic analysis for wheat chromosome 3B (Glover et al, 2015), which is syntenic to sorghum chromosome 3. As no detailed synteny analysis between wheat and sorghum has been done for the remaining chromosomes, the location of sorghum qGI-1, 4, 6,7 and 9 in rice chromosomes was assessed using the Gramene tool for synteny analysis, and then the regions identified in rice were compared to wheat main PHS QTL as described by Cabral et al (2014).…”