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.