Development of a High-Density SNP-Based Linkage Map and Detection of QTL for β-Glucans, Protein Content, Grain Yield per Spike and Heading Time in Durum Wheat

Abstract

High-density genetic linkage maps of crop species are particularly useful in detecting qualitative and quantitative trait loci for important agronomic traits and in improving the power of classical approaches to identify candidate genes. The aim of this study was to develop a high-density genetic linkage map in a durum wheat recombinant inbred lines population (RIL) derived from two elite wheat cultivars and to identify, characterize and correlate Quantitative Trait Loci (QTL) for β-glucan, protein content, grain yield per spike and heading time. A dense map constructed by genotyping the RIL population with the wheat 90K iSelect array included 5444 single nucleotide polymorphism (SNP) markers distributed in 36 linkage groups. Data for β-glucan and protein content, grain yield per spike and heading time were obtained from replicated trials conducted at two locations in southern Italy. A total of 19 QTL were detected in different chromosome regions. In particular, three QTL for β-glucan content were detected on chromosomes 2A and 2B (two loci); eight QTL controlling grain protein content were detected on chromosomes 1B, 2B, 3B (two loci), 4A, 5A, 7A and 7B; seven QTL for grain yield per spike were identified on chromosomes 1A, 2B, 3A (two loci), 3B (two loci) and 6B; and one marker-trait association was detected on chromosome 2A for heading time. The last was co-located with a β-glucan QTL, and the two QTL appeared to be negatively correlated. A genome scan for genomic regions controlling the traits and SNP annotated sequences identified five putative candidate genes involved in different biosynthesis pathways (β-glucosidase, GLU1a; APETALA2, TaAP2; gigantea 3, TaGI3; 14-3-3 protein, Ta14A; and photoperiod sensitivity, Ppd-A1). This study provides additional information on QTL for important agronomic traits that could be useful for marker-assisted breeding to obtain new genotypes with commercial and nutritional relevance.

Non-Starch Polysaccharides in Durum Wheat: A Review

“…The kit includes an industrial standard for barley (4.1% (1,3;1,4)-β-glucan). As mentioned before, (1,3;1,4)-β-glucans are a relatively minor component of durum wheat grain, so investigations of durum genotypes with higher amounts [46][47][48] or wheat-related species such as Aegilops ssp. have been carried out [46,[49][50][51][52][53][54][55] for further genetic-molecular analysis and for the analysis of possible interspecific gene transfer.…”

“…Here we report data from marker trait association for the identification of QTL associate to (1,3;1,4)-β-glucan content in durum kernel and controlling the trait in recombinant inbred lines of a durum population through a classical association mapping approach [48,56] and genome-wide association studies (GWAS) carried out on a collection of tetraploid wheats [47]. A total of 14 QTL have been identified and are distributed across most durum chromosomes ( Figure 2, Table 2), with the highest number on chromosome group 2 [47,48]. Some of the markers associated with the trait are located in the QTL regions containing genes encoding for glycosyl transferase (GT) and glycosyl hydrolase (GH) enzymes.…”

Mapping Agronomic and Quality Traits in Elite Durum Wheat Lines under Differing Water Regimes

“…Single nucleotide polymorphism (SNP) markers are commonly used in quantitative trait loci (QTL) mapping experiments [32,33] and genome-wide association studies (GWAS) for the detection of marker-traits associations (MTAs) in wheat [34][35][36][37][38]. DArTseq, a variant of the microarray-based DArT technology, has also been widely used in QTL mapping [39][40][41].…”

Participation of Wheat and Rye Genome in Drought Induced Senescence in Winter Triticale (X Triticosecale Wittm.)

“…Plant senescence is a process controlled by multiple genes [51]. Some of them encode enzymes responsible for protein degradation [1], protein processing [52], N mobilization [53], lipid degradation [54], C mobilization [1], cell wall degradation [55], P mobilization [56], transport [57], transcriptional regulation [58], signaling pathways [59], antioxidants [7], metal binding [60], hormone biosynthesis [61], cell death [62], defense-related genes [52], translation [63] and some proteins of unknown functions [64]. These proteins involve also those related to carbohydrate metabolism, such as isocitrate lyase, malate synthase, pyruvate orthophosphate dikinase, sugar transporter, endoxyloglucan transferase or β glucosidase [51,65].…”