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.
Black rice is a nutrient-dense whole grain in which anthocyanins accumulate predominantly in the outer caryopsis layers, but stronger pigmentation may impose carbon, energy and precursor demands that compromise yield, stress resilience and grain quality. This review synthesizes molecular and physiological controls of rice anthocyanin accumulation. It systematically evaluates whether relationships among anthocyanin content, grain yield, and eating, processing and nutritional quality are synergistic, antagonistic or unresolved. We present a targeted rather than constitutive biofortification framework integrating rice evidence on phenylpropanoid–flavonoid metabolism and the MYB–basic helix–loop–helix–WD40 transcriptional complex with candidate mechanisms involving epigenetic and post-transcriptional control, vacuolar transport and environmental signalling. Rice studies establish the roles of core pigmentation genes and document variation in grain anthocyanin composition. However, quantitative contributions of auxiliary regulators, transport pathways and environmental signalling remain incompletely validated in black-rice caryopses. We distinguish direct rice-grain evidence from other rice-tissue evidence and from cross-species or source–sink hypotheses. Both require grain-specific causal and field validation. We distinguish two breeding scenarios. One improves existing black-rice cultivars with endogenous, spatially organized pigmentation pathways. The other reconstructs grain-specific anthocyanin production in elite white-rice backgrounds and may require coordinated pathway completion and tighter control of tissue specificity and metabolic burden. We propose a Genotype × Environment × Management framework integrating spatial multi-omics, rice-specific validation, targeted editing, inducible regulation and precision agronomy. Restricting anthocyanin synthesis to appropriate tissues, developmental windows and carbon-replete conditions may improve nutritional value while maintaining yield stability, end-use quality and climate resilience.
This study identified a major QTL governing leaf shape, pinpointed a highly associated SNP, and developed a dCAPSmarker, providing a useful molecular tool to facilitate marker-assisted breeding for leaf shape in soybean. Optimizing plant architecture to enhance canopy light distribution is a central objective in modern crop breeding. Leaf shape is a critical determinant of canopy structure and yield potential, yet the natural genetic variation underlying this trait in soybean remains underexploited for marker-assisted improvement. Here, we performed a genome-wide association study (GWAS) of leaf shape using a panel of 450 soybean accessions from northern China and identified a robust quantitative trait locus (qLS) for leaf shape on chromosome 20 that was consistently detected across multiple statistical models and two consecutive years. The lead SNP (SNP_35828042) resides within the second exon of GmJAG1 encoding a C2H2-type zinc finger transcription factor homologous to Arabidopsis JAGGED. This non-synonymous G/C variation results in an aspartic acid to histidine substitution (D9H) within the highly conserved EAR motif. Analysis of previously generated Cas9-edited GmJAG1 plants provided functional support for the role of GmJAG1 in regulating leaf shape. Population-level analysis revealed northward enrichment of the narrow-leaf-associated C allele, a pattern consistent with regional differentiation. We further developed a derived cleaved amplified polymorphic sequence (dCAPS) marker targeting the G/C polymorphism, which showed complete concordance with visual leaf-shape classification in the 41 tested accessions. This work provides population-scale validation of a GmJAG1-associated polymorphism, characterizes its geographical distribution, and delivers a practical molecular marker for screening soybean germplasm for leaf shape.
Screening global wheat germplasm with a diverse collection of pathogen races expands the catalog of novel Yr loci and identifies new sources of broad-spectrum resistance against evolving Pst populations. Newly emerging highly virulent races of Puccinia striiformis f. sp. tritici (Pst) often defeat deployed resistance genes (Yr), highlighting the need for novel sources of durable resistance. A global diversity panel of 377 spring wheat (Triticum aestivum L.) lines was screened for all-stage resistance (ASR) against a panel of diverse 20 Pst isolates at the seedling stage and for adult-plant-stage resistance (APR) against natural mix of field races. Genome-wide association mapping identified 77 unique Yr loci. Of these, 34 overlapped with the previously mapped 1150 Yr loci, confirming the robustness of our GWAS results, while 43 were likely novel. Comparison of the nine adult-plant-stage Yr loci mapped in our study with known APR genes identified only one overlap, with Yr29. Except for Yr29, APR genes Yr18 and Yr36 were detected at low frequencies, indicating that resistance in our panel may arise from less characterized or novel sources. Two wheat lines, lacking widely effective Yr5 and Yr15 alleles, exhibited resistance to all 20 Pst races at the seedling stage and natural field races at the adult stage, suggesting that they may carry novel, broad-spectrum ASR alleles. Wheat improvement had no effect on the frequency of ASR alleles but resulted in a threefold increase in the frequency of APR alleles, suggesting that the latter were subjected to more consistent breeding selection over time. Our findings underscore the value of combined screening of diverse germplasm with diverse pathogen races to identify novel sources of broad-spectrum resistance for breeding stripe rust resistant cultivars.
Integrating high-throughput phenotyping with multiple complementary GWAS models reduces method-dependent bias and enables reliable identification of novel loci and elite germplasm for durable yellow and leaf rust resistance in wheat. The causal agents of yellow and leaf rust in wheat, Puccinia striiformis f. sp. tritici and Puccinia triticina, pose a serious threat to grain yield and quality worldwide. Growing durable resistant wheat cultivars is an effective protection measure contributing to sustainable agriculture. Many of the known resistance genes, however, have been overcome due to the high genetic diversity and adaptability of pathogen populations. Therefore, the present study aimed to identify novel loci associated with yellow rust and leaf rust in a genome-wide association study using 1984 spring wheat accessions from the German Federal ex situ Genebank. Phenotypic data obtained from a detached-leaf assay were combined with 90,283 genotyping-by-sequencing genome-wide markers. Six significant peak marker-trait associations were identified for yellow rust and leaf rust, respectively. These are located on chromosomes 1D, 2B, 3B, 4A, 4B, 4D, 5A, 6B, and 7D. Six candidate genes were identified close to the identified loci. These findings may be valuable for identifying and deploying genetic resources to broaden the genetic basis of resistance and safeguard durability of resistance against yellow and leaf rust.
