Genome-Wide QTL Mapping for Wheat Processing Quality Parameters in a Gaocheng 8901/Zhoumai 16 Recombinant Inbred Line Population

Abstract

Dough rheological and starch pasting properties play an important role in determining processing quality in bread wheat (Triticum aestivum L.). In the present study, a recombinant inbred line (RIL) population derived from a Gaocheng 8901/Zhoumai 16 cross grown in three environments was used to identify quantitative trait loci (QTLs) for dough rheological and starch pasting properties evaluated by Mixograph, Rapid Visco-Analyzer (RVA), and Mixolab parameters using the wheat 90 and 660 K single nucleotide polymorphism (SNP) chip assays. A high-density linkage map constructed with 46,961 polymorphic SNP markers from the wheat 90 and 660 K SNP assays spanned a total length of 4121 cM, with an average chromosome length of 196.2 cM and marker density of 0.09 cM/marker; 6596 new SNP markers were anchored to the bread wheat linkage map, with 1046 and 5550 markers from the 90 and 660 K SNP assays, respectively. Composite interval mapping identified 119 additive QTLs on 20 chromosomes except 4D; among them, 15 accounted for more than 10% of the phenotypic variation across two or three environments. Twelve QTLs for Mixograph parameters, 17 for RVA parameters and 55 for Mixolab parameters were new. Eleven QTL clusters were identified. The closely linked SNP markers can be used in marker-assisted wheat breeding in combination with the Kompetitive Allele Specific PCR (KASP) technique for improvement of processing quality in bread wheat.

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 genetic length of this map was 2875.3 cM, similar to reported maps in hexaploid wheat (Somers et al, 2004; Wu et al, 2015b). Notably, the high number (11,646) of polymorphic SNP markers between Y8679 and J411 is comparable to Jin et al (2016) and Perez-Lara et al (2016), who detected 12,205 and 10,342 polymorphic SNPs between two parental lines, respectively. Collectively, these data suggest that the iSelect 90K array is a powerful tool for genotyping analysis in hexaploid wheat.…”

“…Collectively, these data indicated that both the iSelect 9K and 90K arrays have considerable limitations when dealing with the D genome. Therefore, studies focusing on chromosomes from the D genome are recommended to use much larger genotyping platforms, such as the recently developed 660K SNP chip (Jin et al, 2016). …”

Comparative Population Genomics of Bread Wheat(Triticum aestivum)Reveals Its Cultivation and Breeding History in China

“…13b and c). We also found that a flour-quality QTL 52 overlaps with a selected region on chromosome 6B.…”

“…Using F ST -θ π , XP-EHH, and XP-CLR analyses, we identified 22.75-Mb (covering 1,760 genes), 3.00-Mb (covering 1,074 genes), and 21.04-Mb (covering 2,619 genes) putatively selected regions between the European and West Asian landraces, respectively (Supplementary Table 10). These selected regions overlap with a few reported QTLs, including two associated with flour quality 52 . We identified a significantly selected region on chromosome 2B that contains TaNPF6.1-2B , another ortholog of the Arabidopsis nitrate transporter gene NRT1.1 (Supplementary Fig.…”

Deciphering the Genetics of Major End-Use Quality Traits in Wheat

“…Performing these evaluations at a late stage in the breeding program often results in ostensibly promising wheat lines with high yield and resistance to diseases that cannot be released due to poor end-use quality traits, such as a weak performance for milling parameters and baking properties. To address these challenges, many studies have been conducted to identify quantitative trait loci (QTL) and associated markers for end-use quality traits, with the aim to use such markers in marker-assisted selection (MAS) to improve quality traits in early generations of the breeding program (Campbell et al 2001; Groos et al 2003; Prasad et al 2003; Breseghello et al 2005; Kulwal et al 2005; Arbelbide and Bernardo 2006; Breseghello and Sorrells 2006; Huang et al 2006; Kuchel et al 2006; Kunert et al 2007; Mann et al 2009; Tsilo et al 2010; Zhao et al 2010; Carter et al 2012; Li et al 2012a; Simons et al 2012; El-Feki et al 2013; Mergoum et al 2013; Deng et al 2015; Echeverry-Solarte et al 2015; Tiwari et al 2016; Jin et al 2016). It should be mentioned that MAS for end-use quality traits would be commenced from F 5 generation onwards if a single seed decent (SSD) method is used to develop wheat cultivars.…”