Resolving a QTL complex for height, heading, and grain yield on chromosome 3A in bread wheat

Abstract

Crop height (Ht), heading date (Hd), and grain yield (GY) are interrelated in wheat. Independent manipulation of each is important for adaptation and performance. Validated QTL for all three collocate on chromosome 3A in the Avalon x Cadenza population with increased Ht, Hd, and GY contributed by Cadenza. We asked if these are linked or pleiotropic effects using recombinant lines and showing that Ht and Hd effects are independent. The Chinese Spring equivalent to the newly defined Ht interval contained a gene cluster involved in cell wall growth and displaying high levels of differential transcript expression. The Hd locus is larger and rearranged compared to the reference genome but FT2 (Flowering Locus T2) is of particular interest. The Hd effect acted independently of photoperiod and vernalization but did exhibit seasonal genotype x environment interaction. Recombinants were phenotyped for GY in replicated field experiments. GY was most associated with Cadenza alleles for later Hd, supporting physiological studies using the same lines proposing that ‘late’ alleles at this locus increase spike fertility and grain number (GN). The work has uncoupled height from heading and yield and shown that one of very few validated GY QTL in wheat is probably mediated by phenological variation.

Identification of QTLs for wheat heading time across multiple-environments

“…The latter is flanked by two previously reported SSR markers Xbarc45 (Griffiths et al 2009) and WMC264 (Zanke et al 2014), but as shown they are located at different positions in the genome being far apart from TaHd044. Similarly, in a quite different part of chromosome 3A is the QTL reported by Martinez et al (2021). Nevertheless, the QTL on 3AL that might overlap with the interval of TaHd044 is detected by Luján Basile et al (2019).…”

Identification and characterization of a natural polymorphism in FT-A2 associated with increased number of grains per spike in wheat

“…An additional QTL for DTH was identified in the Avalon x Cadenza population (U.K.) on chromosome arm 3AS around the peak marker BS00021976 (169 Mb RefSeq v1.0) (Martinez et al 2021 ). This QTL interval (60 Mb at each side of BS00021976) includes 536 annotated genes, among which the authors proposed FT-A2 as a candidate of particular interest.…”

“…Using our FT-A2 marker, we established that both Avalon and Cadenza carry the A10 allele, so we conclude that the D10A polymorphism is not the cause for the observed QTL for DTH on 3AS in this population. Martinez et al ( 2021 ) suggested that differences in FT-A2 transcript levels may contribute to the differences in DTH, but more precise mapping of this QTL will be necessary to support this hypothesis.…”

Genome‐wide association mapping of agronomic traits and grain characteristics in spring wheat under conventional and organic management systems

“…The physical positions of one of the genomic regions that we identified for heading on chromosome 5B (at 575.8 Mb) and the coincident region associated with both heading and GPC on 5A (at 586.5-588.6 Mb) coincided with the Vrn-B1 and Vrn-A1 genes, respectively. Coincident genomic regions and QTLs have been reported in several other studies (Babu et al, 2003;Lanceras et al, 2004;Quarrie et al, 2006;Pushpendra et al, 2007;Bai et al, 2013;Guan et al, 2018), which could be due to the pleiotropic effect (a single locus having effects on more than one trait simultaneously) or tight linkage (Tuberosa et al, 2002;Martinez et al, 2021).…”