This study is to excavate spike length (SL)-related quantitative trait loci (QTL) with potential breeding value, explore the genetic relationship between SL and other important agronomic traits in wheat, and aim at laying a foundation for fine mapping and molecular-assisted selection breeding.

A total of 126 F₇ recombinant inbred lines (RIL) constructed by crossing 20828 and SY95-71 were used in this study. The RIL population including their parents were planted in seven different environments for phenotypic evaluation: Wenjiang, Chongzhou, Ya'an of Sichuan Province in China, and Khulna in Bangladesh during 2016-2017 and 2017-2018 growing seasons. Unconditional QTL mapping was performed using a genetic linkage map constructed using the wheat 55K SNP array, and QTLs' effects were further analyzed. Conditional QTL analysis was performed to analyze the relationship between SL and other agronomic traits including plant height (PH), spike extension length (SEL), spikelet number per spike (SNS) and thousand-kernel weight (TKW).

Thirteen QTLs controlling SL were identified using unconditional QTL mapping, and they were located on chromosomes 1A, 1D, 2B, 2D, 4B, 6D, and 7A. The LOD values ranged from 2.79 to 6.19, and the phenotypic variation rate ranged from 5.35% to 12.77%. Three stable and major QTLs (QSl-sau-2SY-2B, QSl-sau-2SY-2D.5 and QSl-sau-2SY-4B) were identified, and they explained 6.54% to 11.72%, 10.16% to 12.57%, and 5.35% to 10.92% of phenotypic variation rate, respectively. Furthermore, these three major QTLs could be also detected in multi-environment analysis. Moreover, aggregation analysis suggested that the SL of lines polymerizing the positive allels at these three major QTLs was significantly longer than that of those with any two ones or those carrying only one. Meanwhile, it was found that QSl-sau-2SY-2B had no significant effect on PH, SEL, SNS and TKW. QSl-sau-2SY-2D.5 had a significant effect on improving TKW (3.98%), but no significant effect on PH, SEL and SNS. QSl-sau-2SY-4B had a significant effect on decreasing PH (-12.28%) and SEL (-22.26%), but no significant effect on SNS and TKW. The conditional QTL analysis showed that QSl-sau-2SY-2B was independent of PH and SEL, whereas, affected by SNS and TKW. QSl-sau-2SY-2D.5 was independent of SEL, SNS and TKW, but affected by PH. QSl-sau-2SY-4B was independent of SEL and TKW, but affected by PH and SNS.

In this study, three stable and major QTLs were identified for SL: QSl-sau-2SY-2B, QSl-sau-2SY-2D.5, and QSl-sau-2SY-4B, among which QSl-sau-2SY-2B may be a novel QTL independent of PH and SEL.

There is a close relationship between plant height (PH) and yield. The aim of this study is to further explore quantitative trait loci (QTL) of PH with breeding value in wheat and analyze the genetic effects of major QTL for PH on other yield related traits toward to providing a theoretical basis for molecular breeding.

A recombinant inbred line population (MC) derived from a cross between the natural mutant msf and Chuannong 16 (CN16) was used for QTL analysis. During 2020 to 2022, planting and PH phenotype identification were conducted at five environments in Wenjiang, Chongzhou, and Ya’an of Sichuan Province. The high-quality genetic linkage map constructed using the 16K SNP array was used for QTL mapping of PH. Genotypes of flanking markers of major QTL for PH were used to analyze the genetic effects of positive alleles on yield related traits and evaluate the potentiality of QTL for yield improvement.

Eight QTL controlling PH were identified on chromosomes 1A, 3D, 4D, 5A, and 7B, respectively. Among them, two stable and major QTL, QPh.sau-MC-1A and QPh.sau-MC-5A, were located, which explained 9.09% to 25.56% and 3.91% to 13.09% of the phenotypic variation rate, respectively. Their positive alleles were all from CN16. The additive effect analysis showed that PH of the lines carrying positive alleles from QPh.sau-MC-1A and QPh.sau-MC-5A was significantly higher than that of the lines carrying only a single positive allele or none. Correlation analysis showed that PH has a significantly positive correlation with effective tiller number (ETN), a significantly negative correlation with flag leaf width (FLW), and no significant correlation with kernel number per spike (KNPS), kernel weight per spike (KWPS), thousand kernel weight (TKW), flag leaf length (FLL) and anthesis date (AD). Genetic effects analysis showed that positive allele of QPh.sau-MC-1A had a significant effect on improving ETN (56.51%), a significant effect on decreasing KNPS (-11.26%), KWPS (-13.04%), TKW (-5.47%), and FLW (-2.85%), and a significant effect on advancing AD (-0.61%). Positive allele of QPh.sau-MC-5A had a significant effect on improving ETN (10.57%), KNPS (4.32%), and TKW (2.92%), and a significant effect on delaying AD (1.07%).

A major QTL QPh.sau-MC-5A for PH was mapped on chromosome 5A, and its positive allele significantly increased ETN, KNPS, and TKW, indicating that it may have a positive impact on yield.