Genetic dissection of complex traits by quantitative trait locus (QTL) analysis permits the understanding of the genotypic effects of QTL, interactions between QTLs, and QTL-by-environment interactions in wheat. This study aimed to identify the QTL linked to yield, its components, end-use quality traits including kernel, flour, and dough rheology, and related agronomic traits under dryland and irrigated conditions. A mapping population of 179 F_2:6 recombinant inbred lines (RILs) derived from ‘TAM 111’/‘TX05A001822’ was evaluated for these traits to investigate their genetic stability and phenotypic plasticity using 2658 single nucleotide polymorphisms (SNPs) with 35 linkage groups. Traits associated with chromosome regions were detected for individual and across-environment QTL by inclusive composite interval mapping. A total of 30 QTL regions were identified, including 14 consistent QTLs mapped on 11 chromosomes and six pleiotropic QTLs mapped on 5 chromosomes. Three consistent QTLs in chromosomes 1A, 3B, and 6D might be novel. Three major QTLs with both consistent and pleiotropic effects were co-localized with known genes. The first QTL for dough mixing properties was physically clustered around Glu-D1 and had an phenotypic variation explained (PVE) up to 31.3%. The second QTL for kernel-related traits was physically close to the TaCWI-4A (cell wall invertase) gene, which influences the thousand kernel weight, heading date, and harvest index, with a PVE of up to 12.3%. The third QTL, which was colocalized with the TaCWI-5D gene for kernel traits, was identified with a PVE of 6.7%. Epistasis was also detected, but major QTLs were not involved in significant epistasis or interactions with environmental effects. The current study provided new information that is useful for enhanced wheat breeding, which will benefit from the deployment of the favorable alleles for end-use quality, yield, and other agronomic traits in wheat-breeding programs through marker-assisted selection.

Background: Improving grain yield in wheat remains a top priority, requiring integrated breeding and genetic strategies. This complexity poses a major challenge, driven by quantitative polygenic inheritance, environmental influence, and intricate genetic interactions. We investigated genetic factors and their interactions for agronomic and yield traits in two high-yielding winter wheat cultivars adapted to the US Southern Great Plains. Methods: A bi-parental mapping population consisting of 221 F₇ recombinant inbred lines (RIL) derived from ‘TAM 204’ and ‘Iba’ was evaluated for three years in 11 Texas environments. Both parents and RIL population were genotyped on Illumina NovaSeq 6000 and sequences were aligned to IWGSC RefSeq v1.0 using Bowtie2 for SNP calling. For QTL analyses, each trait was analyzed by individual environment, across multiple environments and mega-environments. Results: A total of 86 QTL were mapped for five traits and among them 32 were consistent in more than one environment or analysis. Among consistent QTL, four were pleiotropic to more than one agronomic or yield traits mapped on chromosomes 2B (57.18, 59.47 Mb) and 2D (29.34, 40.64 Mb). The consistent QTL on chromosome 2D (29.34 Mb) was pleiotropic to GYLD, DTH, TW, TKW and explained maximum phenotypic variation for all traits, representing photoperiod gene (Ppd-D1). Another QTL on chromosome 2D (40.64 Mb) was pleiotropic to GYLD and TW and based on the physical position comparisons it likely reflects a unique locus in Iba. The pleiotropic consistent QTL Qgyld.tamu.2B.59 from TAM 204 represents Ppd-B1 gene. Moreover, it is more likely that Qdth.tamu.5B.575 represents the Vrn-B1 gene in Iba. A total of 23 digenic epistatic interactions involved consistent QTL for all traits. Amongst these, epistatic interactions between the consistent QTL on 2B (57.18 Mb) and 2D (29.34 Mb) were observed for GYLD, DTH and TKW. Conclusions: Our findings revealed key allelic diversity and interaction effects in elite wheat cultivars, paving the way for marker development for identified pleiotropic loci and implementation in marker-assisted selection and recombination breeding.

Döl denemeleri, ıslah popülasyonunda yer alan ebeveyn veya döllerin ıslah değerini ve ıslah popülasyonun genetik parametrelerinin tahmini için ıslah çalışmalarında kullanılan genetik testlerdir. Türkiye’de kızılçam ıslah çalışmalarında bu gayeyle çeşitli ıslah zonlarında döl denemeleri kurulmuştur. Akdeniz Bölgesi orta yükselti kuşağı (401-800 m) kızılçam ıslah zonunda bulunan 13 adet tohum meşceresi ve 3 adet gen koruma ormanından toplam 270 adet plus ağaçtan (1. seri) ve 4 adet klonal tohum bahçesinde yer alan 75 klondan (2. seri) toplanan tohumlarla iki ayrı seri halinde açık tozlaşma döl denemeleri kurulmuştur. Deneme alanlarında 20. yaşta gözlemlenen göğüs yüksekliği çapı karakterine ilişkin genetik parametreler ve BLUP yöntemi ile ailelerin ıslah değerleri ve genetik kazançlar tahmin edilmiştir. Birinci seri denemelerin ortak analizinde göğüs yüksekliği çapı için bireysel kalıtım derecesi 0,22±0,03; aile ortalamalarının kalıtım derecesi ise 0,52±0,02 tahmin edilmiştir. İkinci seri denemelerdeki kalıtım derecelerinin tahmini aynı sırayla 0,23±0,06 ve 0,46±0,04 olmuştur. Göğüs yüksekliği çapında ıslah değeri en yüksek 30 ağaç seçildiğinde birinci seride ~%11; ikinci seride ise ~%3 genetik kazanç tahmin edilmiştir.