Aug 2026· Cell Reports· Vol 45, pp.
117779
· 0 citations· 74 references
Medicine
TL;DR
A T2T rapeseed resource and a BnaWRKY44-BnaVPT1 module for breeding high-oil, yellow-seeded rapeseed are provided for breeding high-oil, yellow-seeded rapeseed.
Abstract
Brassica napus yellow-seeded genotypes have higher seed oil content and quality than black-seeded types, but the mechanisms controlling seed coat color (SCC) remain unclear, partly due to limited gap-free references. We generated the telomere-to-telomere genome assembly of the black-seeded cultivar Zhongyou 821 using PacBio HiFi, ultralong ONT, and Hi-C sequencing. Using this reference, genome-wide association study (GWAS) of 504 accessions identified BnaWRKY44 as a major SCC candidate gene. CRISPR-Cas9 knockout of BnaWRKY44 lightened SCC, increased oil content and unsaturated fatty acids, and improved oil quality. Haplotype analysis defined the elite BnaWRKY44Hap4 allele and enabled development of a diagnostic CAPS marker for breeding. Transcriptomic, Y1H and dual-LUC assays showed that BnaWRKY44 directly binds and regulates the BnaVPT1 promoter. BnaVPT1 knockout confirmed its roles in SCC lightening and flavonoid biosynthesis. This work provides a T2T rapeseed resource and a BnaWRKY44-BnaVPT1 module for breeding high-oil, yellow-seeded rapeseed.
Yellow-seeded rapeseed has higher oil content and seed quality than black-seeded varieties, but its genetic basis remains unclear. We report a telomere-to-telomere genome assembly of yellow-seeded rapeseed GH06 (981.18 Mb; contig N50, 56.93 Mb) generated with PacBio HiFi, Oxford Nanopore ultra-long reads, and Hi-C sequencing. The GH06_SWU assembly shows high completeness, accuracy, and continuity, with 110,096 annotated protein-coding genes. Using GH06_SWU, GWAS of seed coat color in 504 accessions identifies a seed coat color-associated BnaSCC1 on chromosome A10. CRISPR-Cas9 knockout of BnaSCC1 inhibits seed coat pigmentation and increases seed oil content (SOC) by 3.37 percentage points on average. Multi-omics analyses show that BnaSCC1 disruption is associated with reduced flavanol glycoside accumulation, elevated triacylglycerol levels, and increased oil body number. Haplotype analysis links BnaSCC1Hap2 with lighter seed coat color, higher oil and oleic acid contents, and lower erucic acid content, supporting its use in marker-assisted breeding.
Haijiang Liu, Kaijie Ye, Yiwen Xie et al.· Cell Reports· 0 citations
Rice (Oryza sativa L.) is a staple crop crucial for global food security, yet its productivity is limited by climate change, diseases, and genetic erosion. The indica cytoplasmic male sterile (CMS) line Funong A (FNA) is an elite breeding resource, exhibiting strong blast resistance, favorable floral traits, and enhanced stem strength through high silica and hemicellulose deposition. Its hybrids demonstrate >10% yield advantages with medium blast resistance, positioning FNA as a pivotal parent for subtropical hybrid breeding. breeding. Here, we present a fully gap-free, telomere-to-telomere (T2T) chromosome-scale genome assembly of FNA. By integrating PacBio HiFi, Oxford Nanopore long reads, and Hi-C sequencing, we produced a 394.7 Mb gap-free assembly with a contig N50 of 32 Mb, capturing all 24 telomeric regions. The assembly demonstrates exceptional accuracy and completeness, including fully resolved centromeres across all 12 chromosomes. We annotated 39,453 protein-coding genes and 1,376 lncRNAs, with the majority of genes functionally characterized. Repetitive elements comprise 51.1% of the genome, reflecting lineage-specific bursts of long terminal repeat retrotransposons. This high-quality T2T genome provides a valuable foundation for dissecting CMS mechanisms, centromere biology, and structural evolution, while offering critical resources for hybrid rice improvement.
In rapeseed (Brassica napus L.), excessive accumulation of flavonoid pigments (anthocyanins/proanthocyanidins) compromises the nutrition, flavor, and commercial value. Therefore, reducing the accumulation of seed coat pigments is one of the main objectives in B. napus breeding. To elucidate the mechanisms affecting the genetic architecture of seed coat color, a genome-wide association study (GWAS) of seed coat color was conducted with a diverse group of 393 B. napus cultivars. NITROGEN LIMITATION ADAPTATION1 (NLA1) was identified as a previously unrecognized regulator that controls seed coat color and participates in flavonoid biosynthesis and accumulation in B. napus. Increasing evidence suggests that BnNLA1 (BnA09NLA1/BnC08NLA1) interacts with and ubiquitinates BnC07MYB3a, an R2R3-MYB-type transcription factor and a candidate regulator of the seed coat color in B. napus, and the lysine residue K164 of BnC07MYB3a is the key ubiquitination. Both the BnA09NLA1/BnC08NLA1 knock-out (KO) mutants and overexpressing BnC07MYB3a lines in B. napus exhibit lighter seed coat color indicating lower anthocyanin and proanthocyanidin accumulation compared with the wild-type plants. BnC07MYB3a also directly binds to the promoter of the TRANSPARENT TESTA 6 (BnTT6) and BANYULS (BnBAN), and represses their expression in B. napus. As expected, the expression levels of BnTT6 and BnBAN are significantly reduced in the BnA09NLA1/BnC08NLA1 KO mutants compared to the wild-type plants. Our findings reveal a novel regulatory framework mediated by the BnNLA1-BnC07MYB3a module for controlling seed coat color in B. napus and provide a new strategy for breeding high-quality B. napus cultivars.
Ran Hu, Haijiang Liu, Yunshan Tang et al.· The Plant Cell· 1 citation
Results indicate that BnaAOG1.A03 and BnaAOG1.C03 are not individually essential for silique and seed development in B. napus, providing a valuable case for functional analysis of homologous genes in polyploid crops.
Jiaxu Xiao, Xiaonan Guo, Aoli Liao et al.· Frontiers in Plant Science· 0 citations
