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.