Yongfu Tao

Key message: The genetic control of GFD in sorghum closely overlaps with that of grain size, is influenced by both pre- and post-anthesis processes, offering new opportunities for yield improvement through targeted breeding and inter-racial trait introgression. The duration of the grain filling period has been associated with yield increases in cereals including maize and sorghum. The genetic control of grain filling duration (GFD) is however not known in sorghum. This study explored the genetic variation and extent of genetic control for GFD in a diverse panel of sorghum genotypes (n=904), in three environments across two years. A genome wide association analysis revealed 86 QTLs, 46 of which collocated with 54 previously reported grain size candidate genes in sorghum, indicating a significant enrichment. Single marker analysis revealed that genomic regions associated with GFD were similarly associated with grain size. Interestingly, in silico expression analysis of candidate genes associated with GFD revealed that GFD could be associated with processes that happen both before and after anthesis contrary to the understanding that GFD was primarily associated with processes that happen post anthesis. Haplotype analysis of SbGS3 resolved 8 haplotypes associated with grain filling duration, 2 of which were exclusive to the Guinea and Asian durra racial groups revealing opportunities for trait introgression across sorghum racial groups. These results indicate considerable opportunity to increase grain yield in sorghum, by selecting for longer GFD and diverse inter racial crosses to improve the genetic diversity for GFD in sorghum. Sorghum breeders will find application of these results in diversifying trait selection to optimise yields in changing environments.

Nucleotide‐binding leucine‐rich repeat (NLR) genes constitute one of the largest families of plant immune receptors and are central to crop disease resistance. Rice ( Oryza sativa L.), maize ( Zea mays L.), and sorghum ( Sorghum bicolor (L.) Moench) are major crops underpinning global food security, and enhancing their immunity is critical for yield stability. Here, we conducted a comprehensive analysis of NLR repertoires across 75 genomes from these three grass crops, identifying 24,944 genes that exhibit extensive intra‐ and interspecific variation. The crops share broadly comparable domain architectures of NLR genes, despite their differences in gene number and genomic clustering pattern. We detected 68 integrated domains, revealing high diversity and pronounced lineage specificity. The pan‐NLR profiles of the three crops were generally similar, with strong lineage‐restricted expansion of NLR gene families. Cross‐species comparisons revealed distinct proportions of common gene and lineage‐specific genes between the crops, suggesting divergent evolutionary trajectories. Widespread presence/absence variation of NLR genes was identified within each crop, with an enrichment in clustered loci. NLRs, especially clustered ones, were significantly enriched in disease‐resistance quantitative trait locus (QTL) hotspots, supporting their critical role in crop disease resistance. Notably, conserved Rp1‐D clusters co‐localized with resistance QTLs in the three crops, underscoring functional conservation and the translational potential of cross‐species NLR studies. Collectively, these findings provide new insights into the genetic diversity and evolutionary dynamics of NLRs in three major grass crops and provide a valuable genomic resource for enhancing crop disease resistance.

Cowpea (Vigna unguiculata L. Walp.) is an Africa-originated legume providing a vital source of protein for millions across resource constrained areas of Africa, Asia and Latin America. Understanding genetic diversity in cowpea is pivotal to its genetic improvement. Here, we assemble 20 high-quality genomes representing cowpea global diversity and construct a graph-based pan-genome to characterize genetic variation. The pan-genome comprises 29,557 orthogroups, with approximately 73% conserved across all accessions. Extensive structural variations (SVs) are uncovered, affecting thousands of coding sequences and gene expression. Thousands of SVs are found under selection between two cowpea subspecies, highlighting their roles in subspecies divergence. We pinpoint key SVs underlying variation in pod length and seed number per pod. Two SV clusters appear to modulate pod length through altering expression and function of VuWAK and VuGA2ox2 genes. These findings provide insights into cowpea genetic diversity and establish a fundamental resource for cowpea genetic improvement.

SUMMARY: Vigna unguiculata (L.) Walp. is a dryland legume crop, providing essential food and nutritional security for millions of people across the semi‐arid tropics, in Africa, Asia and Latin America. However, as a typical ‘orphan crop’, cowpea has long remained underrepresented in global genomic research to support crop improvement. Here, we conducted the largest genetic diversity analysis of cowpea to date, comprising 10 617 accessions sourced from seven international collections. Using genotyping‐by‐sequencing, we characterised the global patterns of genetic diversity, assessed redundancy within and across collections, and examined the geographic structure of the cowpea global allele pool. Our results revealed nine distinct genetic groups with clear geographic associations and fine‐scale population differentiation, reflecting dispersal history, regional adaptation and the influence of modern breeding. Duplication across collections was detected, highlighting the need for improved curation and integration of germplasm resources. Landraces from sub‐Saharan Africa do not fully capture the genetic diversity present in several other geographic regions, indicating the existence of abundant and untapped genetic resources worldwide. These findings not only provide insights into the genetic structure and evolutionary history of cowpea but also offer a valuable foundation for harnessing global germplasm diversity to enhance breeding potential and accelerate crop improvement.

Cowpea (Vigna unguiculata) is a versatile legume crop providing a critical source of grain, vegetable and forage globally. Cultivated cowpea is classified into two main subspecies, subsp. sesquipedalis for fresh-pod vegetable and subsp. unguiculata for grain production. Here, we present two complete telomere-to-telomere (T2T) assemblies for the grain-type inbred lines HJD and vegetable-type FC6 through integrating PacBio HiFi reads, Oxford Nanopore ultralong reads, and Hi-C data. The T2T genomes demonstrated improved contiguity, completeness, and accuracy compared to existing genomes, revealing clear telomeric and centromeric features. Comparative analysis of the T2T genomes highlighted inversions underlying subspecies divergence in cowpea. Evolutionary analysis uncovered contraction of gene families related to symbiosis in HJD, consist with its reduced root nodules compared to FC6. Distribution and composition of tandem repeat arrays and transposable elements in centromeric regions were largely conserved in cowpea, but displayed pronounced variation among Phaseoleae. Furthermore, frequent shifts of centromeric locations coincided with inversions found in Phaseoleae. Overall, this study provides a set of fundamental resources for cowpea improvement and enhances our understanding of cowpea subspecies divergence and genome evolution in Phaseoleae.

Cowpea ( Vigna unguiculata L. Walp.) is an Africa-originated legume providing a vital source of protein for millions across resource constrained areas of Africa, Asia and Latin America. Understanding genetic diversity in cowpea is pivotal to its genetic improvement. Here, we assembled 20 high-quality genomes representing cowpea global diversity and constructed a graph-based pan-genome to characterize genetic variation. The pan-genome comprises 29,557 orthogroups, with approximately 73% conserved across all accessions. Extensive structural variations (SVs) were uncovered, affecting thousands of coding sequences and gene expression. Notably, thousands of SVs were found under selection between two cowpea subspecies, highlighting their roles in subspecies divergence. We pinpointed key SVs underlying variation in pod length and seed number per pod. Two SV clusters appeared to modulate pod length through altering expression and function of VuWAK and VuGA2ox2 genes. These findings provide insights into cowpea genetic diversity and establish a fundamental resource for cowpea genetic improvement.

Sorghum is a versatile crop that serves as a major source of food, feed, fodder and biofuel globally. Lignin content in sorghum affects multiple important traits, including lodging resistance, forage digestibility and the efficiency of bioenergy production. However, the genetic regulation of lignin content in sorghum remains poorly understood. In this study, we combined transcriptomic and comparative genomic approaches to uncover the genetic network underlying lignin biosynthesis in sorghum. Through comparative genomic analysis, we identified 104 candidate genes involved in lignin biosynthesis. Transcriptome analysis of four sorghum accessions with contrasting lignin contents identified 6132 differentially expressed genes with an enrichment of genes related to phenylpropanoid biosynthesis and cell wall biogenesis. The 104 lignin biosynthesis candidates were significantly enriched (p-value < 0.01) in these differentially expressed genes, with most differentially expressed candidate genes related to monolignol biosynthesis and polymerization being up-regulated in high-lignin accessions. These up-regulated genes are related to all key enzymes involved in lignin biosynthesis, suggesting that the elevated lignin content in these accessions results from a collective increase in enzyme activity. Sequence analysis revealed a significant reduction in genetic diversity across lignin biosynthesis genes in cultivated sorghum compared to wild sorghum. Moreover, selection signals during domestication were identified in 30 lignin biosynthesis genes, 22 of which were differentially expressed, further supporting the functional relevance of these differentially expressed genes in lignin biosynthesis. Overall, our findings uncover the lignin biosynthesis gene network in sorghum and offer potential targets for future functional studies and trait manipulation.