Rice tiller number is a key determinant of panicle number and yield, yet its genetic architecture is highly influenced by environmental variation. Identifying loci showing reproducible effects across multiple growing seasons at the same experimental site is important for improving the reliability of GWAS-based locus prioritization for breeding. In this study, 240 rice accessions from the Rice3K panel were evaluated for tiller number over three growing seasons (2021–2023) in Sanya, Hainan Province, representing the South China rice-growing region. Genome-wide association analyses using GLM and MLM, combined with BLUEs, identified reproducible genetic signals. Several previously reported tillering-related genes, such as NAL1, BON3, ANT1, MRG702, D27, WTG1, and VPE2, were detected across different analyses. Among them, NAL1 and ANT1 represented the most consistently associated loci across three growing seasons and statistical models. Gene-based association analysis identified the promoter variants Chr4:31203262 (C/T) in NAL1 and Chr7:7310528 (G/A) in ANT1 as the lead polymorphisms, with the favorable C and G alleles associated with increased tiller number, respectively. In addition, nine putative candidate loci showing suggestive associations across three growing seasons were identified as putative candidate breeding resources. These results highlight the importance of integrating multi-year phenotyping with GWAS to prioritize loci showing reproducible associations across three growing seasons and provide valuable candidate genetic resources for future molecular improvement of rice adapted to the South China rice-growing region.
Root biomass is an important determinant of seedling vigor that contributes to water and nutrient acquisition in rice (Oryza sativa L.). In this study, we evaluated the total root weight (TRW) of 127 Korean rice cultivars, comprising 110 temperate japonica (TEJ) and 17 Tongil-type cultivars, under hydroponic conditions. Population structure analysis separated the accessions into two major groups corresponding primarily to the TEJ and Tongil-type cultivars. A genome-wide association study (GWAS) was conducted using the FarmCPU, BLINK, and MLM approaches, all three of which detected a common association signal for TRW on chromosome 7. Further GWAS analysis using only the 110 TEJ cultivars revealed an association signal in the same genomic region, thereby providing evidence of a possible relationship between this region and the variation in TRW within the TEJ cultivars. Additionally, by performing linkage disequilibrium block analysis, we identified a candidate region spanning approximately 369 kb, containing 43 genes. On the basis of gene expression and haplotype analyses, Os07g0517000, Os07g0520400, and Os07g0520900 were selected as putative candidate genes. However, given that the observed haplotype differences were partially associated with the varietal-group composition, their effects should be interpreted with caution. These results will provide genomic information for gaining a better understanding of variations in seedling root biomass and contribute to further validation of genes associated with root development in rice.
Junghyun Gong, Han-gyeol Kim, Dongryung Lee et al.· Korean Journal of Breeding S...· 0 citations
Rice (
Oryza sativa
L.) is one of the most important staple crops worldwide, and improving grain yield remains a major objective of rice breeding programs. Yield is a complex quantitative trait influenced by multiple agronomic characteristics, including grain yield per plant (GY), seed setting rate (SSR), plant height (PH), and thousand grain weight (TGW). In this study, a natural population comprising 265 rice accessions was evaluated during two consecutive growing seasons (2022-2023) at one field location, and genome-wide association studies (GWAS) conducted using 4454137 high-quality single nucleotide polymorphisms (SNPs). Best linear unbiased prediction (BLUP) values estimated across the two year-environments were used for association analysis using a mixed linear model (MLM). A total of 102 significant SNPs were identified and consolidated into 20 quantitative trait loci (QTLs), including five associated with GY, four with SSR, ten with PH, and one with TGW. Among them, several loci were co-localized with previously reported genes associated with yield related traits, thereby supporting the reliability of the GWAS results. Candidate gene identification and haplotype analysis further revealed four prioritized genes:
LOC_Os09g28230 (GID1L2)
for GY,
LOC_Os05g09500
for SSR,
LOC_Os03g06930
for PH, and
LOC_Os02g09170
for TGW. Significant phenotypic differences among haplotypes supported the potential involvement of these genes in regulating the natural trait variation. These findings provide insights into the genetic basis of rice yield related traits and offer genetic resources for future validation and breeding. However, because the present study included only two year-environments at one field location, additional multi-environment validation is required before the broader environmental reproducibility or breeding adaptation.
Nan-Sheng Wang, M. Hassan, Kang Li et al.· Frontiers in Plant Science· 0 citations
The identified SNPs, alleles, haplotypes, and CGs may be used in marker-assisted selection and breeding programs to develop wheat varieties with enhanced resistance to SB.
G. Singh, Uttam Kumar, Bhagya Shree Acharya et al.· Theoretical and Applied Gene...· 0 citations
Reliable identification of genomic regions controlling complex agronomic traits across variable growing seasons remains a major challenge in soybean genetics and breeding. Here, a diverse panel of 252 soybean accessions was evaluated over six consecutive growing seasons (2018–2023) for flowering time, maturity, plant height, number of seeds per plant, seed yield per plant, and thousand-seed weight. Whole-genome resequencing and variant filtering yielded 2,019,772 high-quality SNPs, and association signals were evaluated using Inclusive Integrative Input Multiple-locus Random-SNP-effect Mixed Linear Model (IIIVmrMLM), Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway (BLINK), and Multi-Locus Mixed Model (MLMM) together with linkage disequilibrium (LD)-based locus consolidation. Cross-model prioritization retained 21 high-confidence loci supported by all three GWAS models and distributed across 10 chromosomes. Among the identified loci, 18 overlapped or co-localized with previously reported SoyBase genes and QTLs, whereas three (q.VER2.13-1, q.YP.01-1, and q.TSW.15-1) showed no positional overlap with known genes and QTLs and were therefore considered presumably novel. These three loci were associated with flowering time, yield per plant, and thousand-seed weight, accounting for 1.60%, 2.13%, and 5.53% of phenotypic variation, respectively. Ten loci co-localized with genomic regions containing established soybean regulators, including E2, E3, GmDt2, and POWR1, support the biological plausibility of the association results. Integration of genomic position, functional annotation, and tissue-expression evidence prioritized 112 candidate genes across 18 loci. These findings provide a focused set of genomic loci and candidate genes for independent validation and further investigation of the genetic basis of soybean adaptation and yield formation under variable continental growing conditions.
A. Zatybekov, Y. Genievskaya, C. Fang et al.· Plants· 0 citations
Sugarcane (Saccharum spp.) is an important crop for food and energy security. Identifying SNPs and genes associated with sugarcane yield and related traits is crucial for developing high ‐ yielding sugarcane cultivars through molecular breeding. Here, we measured nine phenotypic traits across 160 sugarcane genotypes and employed multiple statistical models (namely MLM, CMLM, MLMM, FarmCPU and SUPER) in GWAS to identify stable and pleiotropic loci. A total of 200 SNPs corresponding to 137 QTLs were detected to be significantly associated with nine traits using multiple statistical models, among which 18 QTLs were consistently identified by two or more models. Notably, the SNP S9A_47793177 on chromosome 9A showed the strongest association with phenotypic variation in aboveground biomass, with a phenotypic explanation rate of 70.54%. Additionally, several QTLs significantly associated with tillering ‐ related traits were identified, suggesting that these QTLs may play crucial roles in the regulation of tillering. The QTLs and SNPs identified in this study provide a significant foundation for molecular marker ‐ assisted breeding in sugarcane. This advancement can significantly enhance the efficiency of genetic improvement for sugarcane yield and tillering ‐ related traits.
L. Zhang, C. Xu, J. Li et al.· Plant biology· 0 citations
Net form net blotch (NFNB), caused by
Pyrenophora teres
f.
teres
(
Ptt
), is a major constraint to barley production. However, the genetic basis of adult plant resistance (APR) and seedling resistance remains incompletely understood. This study aimed to dissect the genetic architecture of NFNB resistance in a diverse panel of 273 spring barley accessions.
APR was evaluated in two contrasting field environments in Kazakhstan, whereas seedling resistance was assessed under greenhouse conditions using two
Ptt
races. Genotyping with the 50K SNP array yielded 31,834 high-quality SNPs. Genome-wide association analyses were performed using four models – MLM, MLMM, FarmCPU, and BLINK – that accounted for population structure and kinship. Candidate genes within QTL intervals were prioritized using transcriptomic data from 16 barley tissues and co-expression network analysis.
Substantial phenotypic variation was observed, with moderate heritability for APR (
h
2
= 50.6%) and seedling resistance (
h
2
= 41.3%), together with strong genotype × environment and genotype × race interactions. In total, 275 marker–trait associations were detected for APR and 48 for seedling resistance. These associations were consolidated into 57 genome-wide significant (P < 1.57E–6) or multi-model-supported QTLs across all seven barley chromosomes, including 39 APR and 18 seedling-resistance QTLs. Forty QTLs co-localized with known resistance genes (
Rpt1
,
Rpt2
,
Rpt3
,
Rpt4
,
Rpt6
,
Rpt8
,
Rpt9
, and
SPN1
) or previously reported net blotch QTLs, whereas 17 were potentially novel. Transcriptomic integration identified 87 highly expressed genes within APR QTL regions and 42 within seedling-resistance QTLs. The potentially novel QTLs
Q_NB_1H.6
,
Q_NB_2H.3
, and
Q_NB_3H.1
harbored genes encoding proteins previously associated with pathogen resistance and stress responses. Co-expression analysis revealed stage-specific transcriptional patterns, with APR-associated genes enriched in regulatory functions and seedling-resistance genes enriched in metabolic and structural functions.
The results demonstrate that NFNB resistance is polygenic and developmentally stage-dependent, with partly distinct mechanisms underlying adult plant and seedling resistance. The identified QTLs and prioritized candidate genes provide targets for independent validation, functional characterization, and the development of molecular markers to support breeding for durable NFNB resistance in barley.
Y. Genievskaya, A. Maulenbay, A. Zatybekov et al.· Frontiers in Agronomy· 0 citations
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