Results demonstrated that BnDF3 is a gain‐of‐function allele functioning as the gain‐of‐function BIN2 gene in brassinosteroid (BR) signalling pathway, which may provide both a functional marker and a novel genetic resource useful in variety breeding targeted to strong lodging resistance.
Mao Yang, Yi-Fei Guo, Jiayang Guo et al.· Plant Breeding· 0 citations
Background: Leaf angle is a key determinant of plant architecture and yield under high-density planting. Loss of the ligule reduces leaf angle, offering a strategy for breeding compact maize. This study aims to identify the genetic basis of the liguleless mutant jd30 and develop a functional marker for breeding. Methods: The jd30 mutant was phenotypically characterized and compared with the wild type (WT). Genetic analysis was performed using F2 populations. Map-based cloning was conducted with simple sequence repeat (SSR) and insertion/deletion (InDel) markers. Candidate genes were annotated and sequenced. Allelism tests were performed by crossing jd30 with other lg1 mutants. A Cleaved Amplified Polymorphic Sequence (CAPS) marker was developed based on the causal mutation. Results: The jd30 mutant showed complete ligule loss from the V2 stage onward and had a significantly smaller leaf angle than the wild type. The phenotype is controlled by a single recessive nuclear gene, mapped to a 123-kb interval on chromosome 2 containing four candidate genes. A single-base cytosine (C) deletion at nucleotide 522 of ZmLG1 caused a frameshift and premature stop codon. Two other lg1 mutants, 20292 and 29163, carried distinct mutations—a C insertion and multiple base substitutions, respectively. Allelism tests confirmed jd30 as a novel allele of ZmLG1. A co-dominant CAPS marker, M5, was developed to distinguish wild-type and mutant alleles. Conclusions: This study identifies a novel loss-of-function allele of ZmLG1, designated ZmLG1-1, and the M5 marker, providing valuable genetic resources for modifying leaf architecture and improving maize plant compactness.
Plant height is a key agricultural trait for lodging resistance in maize. To explore key genes regulating plant height, a genome-wide association study (GWAS) was conducted using a large population of 1149 inbred lines. Plant height (PH), ear height (EH), and ear height coefficient (EH/PH) in this population followed a standard normal distribution, with heritability of 86%, 85%, and 75%, respectively. The GWAS identified two significant SNPs (Chr3:163963128 and Chr3:163963155) associated with all three traits. Within a 100-kb genomic region spanning upstream and downstream of the two SNPs, four genes were examined by real-time PCR, and among them, ZmPH1 showed a significant difference between taller lines and shorter lines. ZmPH1 encodes a pentatricopeptide repeat protein. ZmPH1 was also found to colocalize with a mapped PH QTL (qPH3-1) and an EH QTL (qEH3-1) identified in our F2 mapping population. The inbred lines were classified into Hap1 and Hap2 based on the genotype of ZmPH1. Hap1 lines have significantly taller PH and EH than Hap2 lines. A KASP marker designed based on one SNP successfully distinguished tall and short inbred lines after PCR amplification. Subcellular localization analysis showed that ZmPH1 is a chloroplast-localized protein. This study presents a potential PPR gene involved in the regulation of plant height and provides potential genetic resources for maize plant height breeding.
Xiaobo Zhu, Yanyan Wang, Shiyan Liu et al.· Plant physiology and biochem...· 0 citations
Findings elucidate the molecular basis of flowering time in industrial hemp and provide valuable genomic resources for breeding broadly adapted, high-yield varieties.
Lili Tang, Chao Fan, Lie Yang et al.· Scientific Reports· 0 citations
Kernel number per spike (KNPS) is a crucial determinant of wheat yield. Previous studies identified
qKnps-2A
as a major stable QTL for KNPS on chromosome 2A using a recombinant inbred line (RIL) population derived from a cross between the semi-winter wheat cultivar Kenong 9204 and the winter wheat cultivar Jing 411. However, fine mapping and gene cloning of this locus have not been reported.
Using InDel markers developed from parental genomic data, the near-isogenic line (NIL) pairs and 11 key recombinants were identified from residual heterozygous line-derived segregating populations, delimiting
qKnps-2A
to a 5.13 Mb interval (616.30–621.43 Mb) harboring 50 high-confidence genes. Integrated transcriptome sequencing, expression profiling across tissues and developmental stages, sequence comparison, and haplotype analysis identified
TraesCS2A03G0902100
, encoding a zinc knuckle protein, as the most likely candidate gene. Near-isogenic line analysis revealed that the Kenong 9204 allele significantly increased spikelet number per spike (2.94%), floret number per spike (10.51%), and KNPS (14.37%), resulting in a 7.32% yield increase, alongside improvements in grain quality traits. Phytohormone analysis showed the Kenong 9204 allele was associated with elevated IAA and IAA/ABA ratios during early spike development and reduced ABA during late development, suggesting hormone-related physiological changes linked to improved grain set. Haplotype analysis of 314 global accessions showed that Hap-KN9204 was significantly associated with increased KNPS, grain compactness, grain setting, and grain width. This superior haplotype predominates in Asia, Europe, and North America, and is suggestive of positive selection during Chinese wheat breeding, increasing from 30.00% in landraces to 59.62% in modern cultivars.
This study fine-mapped
qKnps-2A
and identified
TraesCS2A03G0902100
as the most likely candidate gene, which was associated with altered phytohormone profiles during spike development, suggesting physiological changes linked to enhanced yield. The superior Hap-KN9204 haplotype appears to have been favored by positive selection in Chinese wheat breeding, establishing
qKnps-2A
as a valuable target for yield improvement.
Meijie Zhu, Yong-Zhen Wu, Guimei Hu et al.· BMC Plant Biology· 0 citations
The height of the first fruiting branch node (HFFBN) is a core indicator for mechanical harvesting of cotton, and the development of molecular markers for this trait is important for accelerating the breeding process. In this study, using bulked segregant analysis coupled with whole-genome sequencing (BSA-seq), one quantitative trait locus (QTL) associated with the HFFBN was mapped; a molecular marker, qFBH7, associated with the HFFBN of cotton was developed; and its application value was systematically evaluated. A total of 20 lines with extreme phenotypes were selected from the recombinant inbred lines constructed using upland cotton Z3-146 and Z3-147 as parental lines. The screened lines with extreme phenotypes were used to construct the extreme high-HFFBN pool and the extreme low-HFFBN pool, which were subsequently used for BSA-seq. Using the upland cotton genome as a reference, relevant QTLs were mapped by BSA-seq. One relevant candidate region was identified, with a total length of 2.25 Mb. The validation experiments revealed that the genotyping results of the KASP_FBH7_03 molecular marker in the parental lines Z3-146 and Z3-147 were completely consistent with the BSA-seq data: Z3-146 had the TT genotype, and Z3-147 had the CC genotype. Among the 66 samples from the natural population, there was a significant difference (p < 0.05) in the HFFBN between the CC and TT genotypes, and the mean HFFBN of the TT genotype was greater than that of the CC genotype. In summary, the KASP_FBH7_03 molecular marker can be effectively used for selective breeding for the HFFBN of cotton, and the TT genotype has a positive regulatory effect on the HFFBN. This study not only provides resources for breeding cotton varieties suited to mechanical harvesting but also offers a robust tool for molecular marker-assisted selection.
Fu-Xiang Zhao, Tao Yang, Xu-Wen Wang et al.· Genes· 0 citations
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