Whole-genome meta-analysis coupled with haplotype analysis reveal new genes and functional haplotypes conferring pre-harvest sprouting in rice DOI Creative Commons
Kelvin Dodzi Aloryi, Benjamin Karikari,

Mawuli Korsi Amenyogbe

и другие.

BMC Plant Biology, Год журнала: 2025, Номер 25(1)

Опубликована: Апрель 25, 2025

Pre-harvest sprouting (PHS), which adversely impacts grain yield and quality, is controlled by seed dormancy genes. However, only a few dormancy-related genes have been characterized, the effects of allelic variation in genetic basis rice remain largely unknown. Here, we performed whole-genome meta-quantitative trait loci study to elucidate rice. One hundred sixty-seven QTL were identified for PHS from 134 successfully projected onto reference map yielding 20 consensus regions, meta-QTL (mQTL). The mean confidence interval mQTL was narrower (9.56-fold reduction) than that initial QTL. Six designated as breeders' based on their small intervals, large phenotypic variance explained, involvement high number Further, retrieved 559 high-confidence regions conferring resistance PHS. Comparative analysis found an RNA-seq-based transcriptomic dataset discovered 34 common Kyoto Encyclopedia Genes Genomes (KEGG) pathway revealed significant enrichment amino sugar nucleotide metabolism, carbon fixation photosynthetic organs. Combined silico expression profiling qRT-PCR validation showed LOC_Os10g18364, LOC_Os10g21940, LOC_Os10g22590, LOC_Os10g25140 exhibited fold-change resistant cultivar (23xS-261) susceptible (23xS-262). Association these with germination rate index demonstrated LOC_Os10g18364Hap1, LOC_Os10g21940Hap1, LOC_Os10g22590Hap1, LOC_Os10g25140Hap1/Hap3 low (GR) cultivars carrying haplotypes. In summary, this delineates provides new set target improving resistance. natural variants markers associated serve potential resources incorporating

Язык: Английский

Identifying key factors influencing maize stalk lodging resistance through wind tunnel simulations with machine learning algorithms DOI Creative Commons

Guanmin Huang,

Ying Zhang, Shenghao Gu

и другие.

Artificial Intelligence in Agriculture, Год журнала: 2025, Номер unknown

Опубликована: Янв. 1, 2025

Язык: Английский

Процитировано

1
Optimizing canopy spacing configuration enhances foxtail millet grain yield and water productivity by improving stalk lodging resistance in the North China Plain DOI

Yuanning Zhong,

Ting Zhang,

Wenjun Qiao

и другие.

European Journal of Agronomy, Год журнала: 2024, Номер 158, С. 127230 - 127230

Опубликована: Июнь 4, 2024

Язык: Английский

Процитировано

5
Unraveling the genetic basis of heat tolerance and yield in bread wheat: QTN discovery and Its KASP-assisted validation DOI Creative Commons
Latief Bashir, Neeraj Budhlakoti,

Anjan Kumar Pradhan

и другие.

BMC Plant Biology, Год журнала: 2025, Номер 25(1)

Опубликована: Март 1, 2025

Wheat (Triticum aestivum L.), a globally significant cereal crop and staple food, faces major production challenges due to abiotic stresses such as heat stress (HS), which pose threat global food security. To address this, diverse panel of 126 wheat genotypes, primarily landraces, was evaluated across twelve environments in India, comprising three locations, two years growing conditions. The study aimed identify genetic markers associated with key agronomic traits bread wheat, including germination percentage (GERM_PCT), ground cover (GC), days booting (DTB), heading (DTHD), flowering (DTFL), maturity (DTMT), plant height (PH), grain yield (GYLD), thousand weight (TGW), the normalized difference vegetation index (NDVI) under both timely late-sown conditions using 35 K SNP genotyping assays. Multi-locus GWAS (ML-GWAS) employed detect marker-trait associations, identified were further validated Kompetitive Allele Specific PCR (KASP). Six ML-GWAS models for this purpose, leading identification 42 highly consistent quantitative trait nucleotides (QTNs) late sown conditions, controlled by 20 SNPs, explaining 3–58% total phenotypic variation. Among these, noteworthy QTNs QTN (qtn_nbpgr_GYLD_3B) on chromosome 3B, pleiotropic AX-95018072 7A influencing phenology NDVI, robust TGW chromosomes 2B (qtn_nbpgr_TGW_2B), 1A (qtn_nbpgr_TGW_1A), 4B (qtn_nbpgr_TGW_4B). Furthermore, annotation revealed that candidate genes near these encoded stress-responsive proteins, chaperonins, glycosyl hydrolases, signaling molecules. Additionally, SNPs (7A), AX-94946941 (6B), AX-95232570 (1B) successfully KASP assay. Our effectively uncovered novel linked tolerance yield-related through an extensive approaches. These not only corresponded previously QTLs but also highlighted several new loci, broadening existing understanding. findings provide valuable insights into basis offer genomic resources, could accelerate marker-assisted breeding development next-generation heat-resilient cultivars.

Язык: Английский

Процитировано

0
Whole-genome meta-analysis coupled with haplotype analysis reveal new genes and functional haplotypes conferring pre-harvest sprouting in rice DOI Creative Commons
Kelvin Dodzi Aloryi, Benjamin Karikari,

Mawuli Korsi Amenyogbe

и другие.

BMC Plant Biology, Год журнала: 2025, Номер 25(1)

Опубликована: Апрель 25, 2025

Pre-harvest sprouting (PHS), which adversely impacts grain yield and quality, is controlled by seed dormancy genes. However, only a few dormancy-related genes have been characterized, the effects of allelic variation in genetic basis rice remain largely unknown. Here, we performed whole-genome meta-quantitative trait loci study to elucidate rice. One hundred sixty-seven QTL were identified for PHS from 134 successfully projected onto reference map yielding 20 consensus regions, meta-QTL (mQTL). The mean confidence interval mQTL was narrower (9.56-fold reduction) than that initial QTL. Six designated as breeders' based on their small intervals, large phenotypic variance explained, involvement high number Further, retrieved 559 high-confidence regions conferring resistance PHS. Comparative analysis found an RNA-seq-based transcriptomic dataset discovered 34 common Kyoto Encyclopedia Genes Genomes (KEGG) pathway revealed significant enrichment amino sugar nucleotide metabolism, carbon fixation photosynthetic organs. Combined silico expression profiling qRT-PCR validation showed LOC_Os10g18364, LOC_Os10g21940, LOC_Os10g22590, LOC_Os10g25140 exhibited fold-change resistant cultivar (23xS-261) susceptible (23xS-262). Association these with germination rate index demonstrated LOC_Os10g18364Hap1, LOC_Os10g21940Hap1, LOC_Os10g22590Hap1, LOC_Os10g25140Hap1/Hap3 low (GR) cultivars carrying haplotypes. In summary, this delineates provides new set target improving resistance. natural variants markers associated serve potential resources incorporating

Язык: Английский

Процитировано

0