Functional markers in wheat: current status and future prospects

Abstract

Functional markers (FM) are developed from sequence polymorphisms present in allelic variants of a functional gene at a locus. FMs accurately discriminate alleles of a targeted gene, and are ideal molecular markers for marker-assisted selection in wheat breeding. In this paper, we summarize FMs developed and used in common wheat. To date, more than 30 wheat loci associated with processing quality, agronomic traits, and disease resistance, have been cloned, and 97 FMs were developed to identify 93 alleles based on the sequences of those genes. A general approach is described for isolation of wheat genes and development of FMs based on in silico cloning and comparative genomics. The divergence of DNA sequences of different alleles that affect gene function is summarized. In addition, 14 molecular markers specific for alien genes introduced from common wheat relatives were also described. This paper provides updated information on all FMs and gene-specific STS markers developed so far in wheat and should facilitate their application in wheat breeding programs.

QTL detection for wheat kernel size and quality and the responses of these traits to low nitrogen stress

“…In this study, QTL mapping analysis showed that the TaCwi-A1a allele may be associated with not only an increased kernel size but also improved kernel milling and baking quality and that it could enhance the tolerance of both quality and yield to N stress. The sucrose synthase 2 (Sus2) gene is associated with wheat yield (Jiang et al 2011;Liu et al 2012;Rasheed et al 2014). In this study, QTL mapping analysis showed that TaSus2 had opposite effects on the yield and quality traits.…”

“…The cell wall invertase (CWI) gene is associated with TKW (Ma et al 2012;Liu et al 2012;Rasheed et al 2014). In this study, QTL mapping analysis showed that the TaCwi-A1a allele may be associated with not only an increased kernel size but also improved kernel milling and baking quality and that it could enhance the tolerance of both quality and yield to N stress.…”

“…Numerous genes associated with simply inherited traits have already been mapped, and corresponding functional makers have been developed (Liu et al 2012). In most cases, the functional marker of a gene is located in very close proximity to the QTL for the same trait (Sourdille et al 2003).…”

“…Glutamine synthetase (GS2) is a key enzyme involved in plant N metabolism that is responsible for the first step of ammonium assimilation and transformation into glutamine; thus, it plays a key roles in the growth, N use and yield potential of cereal crops, including wheat (Gadaleta et al 2011;Li et al 2011). Polyphenol oxidase (PPO) activity is highly correlated with the undesirable browning of wheat-based end products, especially Asian noodles (He et al 2007;Liu et al 2012). TaGS2-D1 and PPO-D1 have been mapped to 210.30 and 214.80 cM on chromosome 2DL in the KJ-RIL map, respectively (Cui et al 2014a).…”

“…Functional or gene-specific markers are derived from polymorphic sites within genes that are directly associated with phenotypic variations (Liu et al 2012). In most cases, a functional marker of a gene co-localizes with the QTL peak position for the same trait (Sourdille et al 2003).…”