Comparative genetic analysis of a wheat seed dormancy QTL with rice and Brachypodium identifies candidate genes for ABA perception and calcium signaling

Abstract

Wheat preharvest sprouting (PHS) occurs when seed germinates on the plant before harvest resulting in reduced grain quality. In wheat, PHS susceptibility is correlated with low levels of seed dormancy. A previous mapping of quantitative trait loci (QTL) revealed a major PHS/seed dormancy QTL, QPhs.cnl-2B.1, located on wheat chromosome 2B. A comparative genetic study with the related grass species rice (Oryza sativa L.) and Brachypodium distachyon at the homologous region to the QPhs.cnl-2B.1 interval was used to identify the candidate genes for marker development and subsequent fine mapping. Expressed sequence tags and a comparative mapping were used to design 278 primer pairs, of which 22 produced polymorphic amplicons that mapped to the group 2 chromosomes. Fourteen mapped to chromosome 2B, and ten were located in the QTL interval. A comparative analysis revealed good macrocollinearity between the PHS interval and 3 million base pair (mb) region on rice chromosomes 7 and 3, and a 2.7-mb region on Brachypodium Bd1. The comparative intervals in rice were found to contain three previously identified rice seed dormancy QTL. Further analyses of the interval in rice identified genes that are known to play a role in seed dormancy, including a homologue for the putative Arabidopsis ABA receptor ABAR/GUN5. Additional candidate genes involved in calcium signaling were identified and were placed in a functional protein association network that includes additional proteins critical for ABA signaling and germination. This study provides promising candidate genes for seed dormancy in both wheat and rice as well as excellent molecular markers for further comparative and fine mapping.

Genome-wide association mapping of preharvest sprouting resistance in a diversity panel of European winter wheats

“…In addition, this chromosome region on chromosome 1A was also found to carry a QTL for seed dormancy in the study of Rehman Arif et al (2012). The marker wPt-408 associated with the highly pronounced QTL for both LS and GI on chromosome 2B was located in the deletion breakpoint interval 2BS1-0.53-0.75 previously reported to harbor QPhs.cnl-2B.1 (Somyong et al 2011). Regarding the pure seed dormancy QTL on the long arm of chromosome 2B, Kulwal et al (2012) found the concurrent association between wPt-697 and seed dormancy.…”

QTL Analysis of Spike Morphological Traits and Plant Height in Winter Wheat (Triticum aestivum L.) Using a High-Density SNP and SSR-Based Linkage Map

“…The primary utility of gene-based linkage maps is for comparative mapping, which has become a tool for comparing gene order and content across related grass species (Somyong et al, 2011). A number of successful studies have reported the fine mapping of QTLs for agronomically important traits based on orthologous regions across several grass species (Chen et al, 2007; Handa et al, 2008; Somyong et al, 2011).…”

Wheat grain preharvest sprouting and late maturity alpha-amylase

“…Not a simple task in view of the numbers of individuals that would need to be tested, the difficulties in phenotyping, and the need to retain a host of other traits required in a commercial wheat variety. Major QTL that have been validated by several researchers in different germplasm are located on chromosomes 4A (Kato et al 2001;Mares and Mrva 2001;Mares et al 2005;Flintham et al 2002), 3AS (Osa et al 2003;Mori et al 2005) and 2B (Muncvold et al 2009;Chao et al 2010;Somyong et al 2011). Tightly linked or diagnostic markers have been developed for these QTL however, a substantial proportion of observed genetic variation remains unexplained ) and a combination of phenotyping and genotyping is required to recover the full dormancy at least from some sources.…”

“…By contrast, the QTL on the distal end of 3AS is reported to be co-localized with wheat homologue of Mother of FT and TFL1 (MFT) which appeared to be upregulated in dormant seeds grown at lower temperature (Nakamura et al 2011;Liu et al 2013a). The QTL on 2B has been fine mapped and a potential candidate gene, a putative ABA receptor, identified (Somyong et al 2011). Zhang et al (2014) cloned a wheat ortholog of the rice dormancy gene, OsSdr4, and whilst it was reported to reside in a similar chromosome interval as the 2B QTL described by (Muncvold et al 2009) it explained only a small proportion of the observed variation in dormancy phenotype.…”