Plant height is a key agronomic trait in wheat that influences both yield potential and lodging resistance. It is primarily determined by the elongation of stem internodes. This study aimed to systematically evaluate the internode lengths of 224 Sichuan wheat cultivars, identify stable quantitative trait loci (QTL) regulating internode length and clarify their effects on agronomic traits, and screen the underlying candidate genes, thus providing important genetic resources and a theoretical basis for the targeted breeding of high-yield wheat varieties.

The lengths of the first (IL1), the second (IL2), and the third (IL3) internodes were measured under two different environments. The panel was genotyped using the wheat 120K SNP array. A genome-wide association study (GWAS) was employed to identify QTL regulating internode length. The phenotyping data was used for correlation analysis and the interpretation of the genetic effects of major QTL. The candidate genes of the major QTL were predicted based on wheat omics data.

Phenotypic analysis revealed continuous variation for all internode traits, with high broad-sense heritability estimates ranging from 75% to 89%. Correlation analysis showed that lengths of all three internodes were positively correlated with final plant height, with IL1 exhibiting the strongest correlation. Furthermore, IL2 and IL3 were highly correlated with each other, suggesting coordinated genetic regulation of the lower stem internodes. GWAS detected four stable QTLs on chromosomes 5A and 4D, namely QIL1.sau.5A for IL1, two tightly linked but distinct QTL QIL2.sau.5A.1 and QIL2.sau.5A.2 for IL2, and QIL3.sau.4D for IL3, respectively. Pleiotropy analysis demonstrated that QIL2.sau.5A.1 significantly increased plant height and spike length, while QIL3.sau.4D primarily promoted internode elongation and overall plant height. Based on functional annotation and spatiotemporal expression data, five candidate genes potentially involved in transcriptional regulation, hormone signal transduction, and cell growth were identified.

This study elucidated the genetic architecture of internode elongation in a panel of Sichuan wheat cultivars and identified two novel QTLs and several pleiotropic loci. These stable QTLs and the underlying candidate genes provided valuable resources for molecular marker-assisted selection aiming at optimizing plant height, improving lodging resistance, and enhancing yield potential in wheat.

As a critical component of wheat grains, the embryo is closely correlated to nutritional value, germination, and seedling establishment. Mining embryo size loci from genetically diverse Chinese wheat landraces and deciphering their genetic effects will enhance our understanding of the genetic basis of embryo size and provide molecular targets for future breeding programs.

We genotyped 240 Chinese wheat landraces using the 660K SNP array and performed genome-wide association studies (GWAS) via a mixed linear model, integrating embryo size phenotypic data across three environments. Significant loci were subjected to genetic effect analysis and candidate gene prediction.

Phenotypic variation ranges across environments and BLUP values were: embryo length (1.64-3.43 mm), width (0.93-2.58 mm), area (1.10-5.71 mm²), and length-to-width ratio (1.06-2.08), with broad-sense heritabilities of 0.76, 0.47, 0.54, and 0.60, respectively. Significant positive correlations (r=0.271-0.922) existed among embryo traits, and between major embryo traits (length, width, area) and grain length or thousand-kernel weight. A total of 18 stable SNP loci significantly associated with embryo length and area were identified across two environments and BLUP values, which were clustered into four quantitative trait locus (QTL) intervals. These included three QTLs for embryo length and one for embryo area, with colocalization observed between QEA.sicau.3B and QEL.sicau.3B.2. For the major QTL QEL.sicau.1B, we predicted nine candidate genes. Genetic effect analysis revealed that the increasing allele of QEL.sicau.1B significantly enhanced embryo length, grain length and width, thousand-kernel weight, and reduced flowering time, while demonstrating superior effects on seedling root dry weight and shoot biomass, albeit with minor negative impacts on tiller number and spikelet number. Comparative analysis suggested both QEL.sicau.1B and QEL.sicau.3B.2 represent novel loci.

GWAS identified four stable loci significantly associated with embryo size, among which nine potential candidate genes were predicted for the major embryo-length QTL (QEL.sicau.1B). The study demonstrated significant positive correlations between embryo size and grain dimensions, and revealed a functional association with seedling root vigor.

Spike density (SD) is an important agronomic trait in wheat, and elucidating its genetic regulatory mechanisms is crucial for constructing ideal spike architecture and achieving yield breakthroughs. This study aimed to identify and genetically characterize key genetic loci controlling SD, providing a theoretical basis for molecular design breeding of wheat spike morphology.

A recombinant inbred line (RIL) population consisting of 198 F₆ lines derived from a cross between the natural mutant msf and cultivar Chuannong16 was used. Combined with a genetic linkage map based on the wheat 16K SNP array, quantitative trait loci (QTL) associated with SD were systematically identified using phenotypic data from four environments. Furthermore, two populations with different genetic backgrounds were employed to validate the major and stably expressed QTL. The genetic effects of the stable QTL on yield-related traits were analyzed, and their potential for yield improvement was evaluated.

The SD of the RIL population ranged from 0.62 to 2.35, with a heritability of 0.71. SD showed a significant positive correlation with productive tiller number and spikelet number, while exhibiting a highly significant negative correlation with grains per spike, grain weight per spike, and spike length. Nine QTLs controlling SD were identified, distributed on chromosomes 1A, 1D, 5A (2 QTLs), 5B, 7A (3 QTLs), and 7B. Among them, QSd.sicau-MC-1A was mapped between flanking markers 1A_1208254 and 1A_3911208 on chromosome 1A and detected in two environments and in the best linear unbiased prediction (BLUP) dataset, explaining 9.05%-15.84% of the phenotypic variation. This QTL, with its positive allele derived from Chuannong 16, was considered a major and stably expressed locus, and its effect was further validated in two independent genetic backgrounds. QSd.sicau-MC-7A.1 was located between markers 7A_671413788 and 7A_672390144 on chromosome 7A and also detected in two environments and BLUP. Although stably expressed, this QTL had a relatively minor effect (7.06%-10.39% phenotypic variation), with its positive allele originating from msf. The remaining seven QTLs were minor-effect loci. Genetic effect analysis revealed that the positive allele of QSd.sicau-MC-1A had negative effects on major yield-related traits, whereas QSd.sicau-MC-7A.1 exhibited positive effects. Additive effect analysis demonstrated that lines carrying both QSd.sicau-MC-1A and QSd.sicau-MC-7A.1 positive alleles had significantly higher SD (9.01% increase) compared to those carrying only one or no positive alleles. Lines with only QSd.sicau-MC-1A or QSd.sicau-MC-7A.1 showed 5.03% and 4.19% increases in SD, respectively, over lines without any positive alleles. Comparative analysis with previously reported SD QTLs suggested that QSd.sicau-MC-1A might be a novel locus.

Two stably expressed QTLs for SD, QSd.sicau-MC-1A and QSd.sicau-MC-7A.1, were identified in wheat. The latter shows greater potential for breeding applications.

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.

This study is to excavate embryo-related quantitative trait loci (QTL) with potential breeding value, to explore the genetic relationship between embryo and other agronomic traits in tetraploid wheat, and finally to aim at laying an important foundation for the fine mapping and breeding utilization of embryo-related traits in the future.

A total of 121 F₈ recombinant inbred lines (RIL) constructed by crossing tetraploid durum wheat (Ailanmai) and wild emmer wheat (LM001) were used. This RIL population was planted in five different environments including Chongzhou (2018-2020), Wenjiang (2020), and Ya'an (2020) in Sichuan Province for phenotypic evaluation of embryo length (EL), embryo width (EW), embryo length/embryo width (EL/EW), embryo length/kernel length (EL/KL), embryo width/kernel width (EW/KW), and embryo area (EA). QTL mapping was performed based on a genetic linkage map constructed based on the wheat 55K SNP.

The embryo size-related traits showed approximately normal distribution in the RIL population satisfying the genetic characteristics of quantitative traits. A total of 27 QTL for embryo size-related traits were detected in five environments over three years. Among them, seven ones controlling EL could contribute 7.75%-21.74% of phenotypic variation. Seven QTLs controlling EW could explain 7.67%-33.29% of phenotypic variation. Five stable and major QTLs (QEL.sicau-AM-3B, QEW.sicau-AM-2B, QEW/KW.sicau-AM-2B, QEL/EW.sicau- AM-2B-1 and QEA.sicau-AM-2B) were identified, and they explained 11.88%-18.99%, 21.77%-29.41%, 8.80%-24.92%, 12.79%- 25.69% and 10.47%-15.22% of phenotypic variation, respectively. In addition, four QTL-rich regions were identified in the embryo size-related loci mentioned above. The QTL controlling EL/KL and EL was located on chromosome 1B, that for EW, EL/EW, EW/KW, and EA was located on 2B, that controlling EL and EA was on 3B, and that controlling EL/EW and EW/KW was on 6B. Embryo size was significantly and positively correlated with kernel size. Further, the major QTL for EL, QEL.sicau-AM-3B was co-located with that for kernel length identified previously, but that for EW QEW.sicau-AM-2B was independent of that for kernel width. Four genes likely involved in regulation of embryo size were identified in intervals where major QTL were mapped.

Five stable and major QTLs were identified: QEL.sicau-AM-3B, QEW.sicau-AM-2B, QEW/KW.sicau-AM-2B, QEL/EW.sicau-AM-2B-1, QEA.sicau-AM-2B, among which QEW.sicau-AM-2B may be novel.

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.

Spike length (SL) plays an important role in determining spike structure and yield potential of wheat. Quantitative trait loci (QTL) for spike length were excavated and their genetic effects were further analyzed to provide theoretical basis for molecular breeding.

This study consisted of a population of 198 F₆ recombinant inbred lines (RIL) derived from the cross between the natural mutant msf and the cultivar Chuannong 16 (MC population). The MC population and its parents were planted in five different environments including Wenjiang in 2021 and 2022 (2021WJ and 2022WJ); Chongzhou in 2021 and 2022 (2021CZ and 2022CZ); and Ya’an in 2021 (2021YA) for spike length measurement. The 16K SNP chip-based constructed high-quality and high-density genetic linkage maps were used to map QTL for spike length. Additionally, the genotype of the flanking markers for the major spike length QTL was used to analyze its genetic effect on yield-related traits and thus to evaluate its potentiality for yield improvement.

A total of 14 QTL for spike length were identified and they were mainly distributed on chromosomes 1A (one), 1B (one), 2B (one), 3D (three), 4A (one), 4D (two), 5A (one), 5B (one), 7A (one), 7B (one), and 7D (one). Among them, QSl.sau.1A was detected in four environments and the best linear unbiased prediction (BLUP) value, explained 6.46% to 20.12% of the phenotypic variation, and thus was regarded as a major QTL. The positive allele at QSl.sau.1A came from the parental line msf. QTL analysis across multiple environments also detected QSl.sau.1A, indicating it exhibits minimal environmental influence and represents a major and stably expressed QTL. The effect of QSl.sau.1A was successfully verified in two populations with different genetic backgrounds. Genetic effects analysis showed that the positive allele of QSl.sau.1A showed a significant effect on improving grain number per spike (12.68%), grain weight per spike (14.99%), 1000-grain weight (5.79%), flag leaf width (2.94%), spikelet number (1.48%), and flowering date (0.61%), and a significant effect of reducing plant height (-6.47%) and effective tiller number (-36.11%).

A major and stably expressed spike length QTL, QSl.sau.1A, was detected on chromosome 1A. Its positive allele significantly increased grain number per spike, grain weight per spike, thousand grain weight, and spikelet number per spike, indicating its great breeding value.