Search

Seed size is variable within many plant species, and understanding the underlying genetic factors can provide insights into mechanisms of local environmental adaptation. Here we make use of the abundant genomic and germplasm resources available for rice (Oryza sativa) to perform a large-scale genome-wide association study (GWAS) of grain width. Grain width varies widely within the crop and is also known to show climate-associated variation across populations of its wild progenitor. Using a filtered dataset of >1.9 million genome-wide SNPs in a sample of 570 cultivated and wild rice accessions, we performed GWAS with two complementary models, GLM and MLM. The models yielded 10 and 33 significant associations, respectively, and jointly yielded seven candidate locus regions, two of which have been previously identified. Analyses of nucleotide diversity and haplotype distributions at these loci revealed signatures of selection and patterns consistent with adaptive introgression of grain width alleles across rice variety groups. The results provide a 50% increase in the total number of rice grain width loci mapped to date and support a polygenic model whereby grain width is shaped by gene-by-environment interactions. These loci can potentially serve as candidates for studies of adaptive seed size variation in wild grass species. Key words: grain size, genome-wide association study (GWAS), General Linear Model (GLM), Mixed Linear Model (MLM), Oryza sativa, rice. La taille des graines est variable chez de nombreuses especes vegetales et comprendre les facteurs genetiques qui sous-tendent cette variation peut fournir un eclairage sur les mecanismes d'adaptation aux conditions locales. Dans ce travail, les auteurs emploient les abondantes ressources genomiques et genetiques disponibles chez le riz (Oryza sativa) pour realiser une analyse d'association pan-genomique (GWAS) a grande echelle sur la largeur des graines. La largeur des graines varie grandement au sein de cette espece et presente une variation associee au climat parmi les populations du riz sauvage. A l'aide d'un jeu filtre de >1,9 million de marqueurs SNP a travers le genome chez 570 accessions de riz cultive et sauvage, les auteurs ont realise un GWAS a l'aide de deux modeles complementaires, GLM et MLM. Les modeles ont livre 10 et 33 associations significatives, respectivement, et ont conjointement revele sept regions candidates, dont deux avaient ete identifiees precedemment. Des analyses de la diversite nucleotidique et de la distribution des haplotypes a ces locus ont revele des signatures de selection et une structure suggerant une introgression adaptative d'alleles pour la largeur des graines parmi les differents groupes du riz. Ces resultats augmentent de 50% le nombre total de locus pour la largeur des graines chez le riz et supportent un modele polygenique ou la largeur des grains est determinee par des interactions gene-environnement. Ces locus pourront possiblement servir de candidats pour de futures etudes sur la variation adaptative au sein des especes sauvages de graminees. [Traduit par la Redaction] Mots-cles: taille des graines, analyse d'association pan-genomique (GWAS), modele lineaire general (GLM), modele lineaire mixte (MLM), Oryza sativa, riz., Introduction Seed size has long been recognized as an important contributor to habitat-specific adaptation in plants (Chapin et al. 1993). Production of larger seeds can provide fitness advantages in unfavorable [...]

The Dong people are one of China's 55 recognized ethnic minorities, but there has been a long-standing debate about their origins. In this study, we performed whole-genome resequencing of Kam Sweet Rice (KSR), a valuable, rare, and ancient rice landrace unique to the Dong people. Through comparative genomic analyses of KSR and other rice landraces from south of the Yangtze River Basin in China, we provide evidence that the ancestors of the Dong people likely originated from the southeast coast of China at least 1000 years ago. Alien introgression and admixture in KSR demonstrated multiple migration events in the history of the Dong people. Genomic footprints of domestication demonstrated characteristics of KSR that arose from artificial selection and geographical adaptation by the Dong people. The key genes GS3 , Hd1 , and DPS1 (related to agronomic traits) and LTG1 and MYBS3 (related to cold tolerance) were identified as domestication targets, reflecting crop improvement and changes in the geographical environment of the Dong people during migration. A genome-wide association study revealed a candidate yield-associated gene, Os01g0923300 , a specific haplotype in KSR that is important for regulating grain number per panicle. RNA-sequencing and quantitative reverse transcription–PCR results showed that this gene was more highly expressed in KSR than in ancestral populations, indicating that it may have great value in increasing yield potential in other rice accessions. In summary, our work develops a novel approach for studying human civilization and migration patterns and provides valuable genomic datasets and resources for future breeding of high-yield and climate-resilient rice varieties. Whole-genome resequencing of Kam Sweet Rice (KSR) and other rice landraces revealed alien introgression and admixture in KSR, providing insights into the origins and migration routes of the Dong people, who traditionally cultivate only KSR. Key genes related to the superior agronomic traits and strong cold tolerance of KSR have been targets of long-term natural and artificial selection, making KSR a valuable resource for future rice breeding. [ABSTRACT FROM AUTHOR]

Ethnic minorities living in Guizhou Province, China, have produced numerous rice landraces that are rich in genetic variations. Studying the genetic diversity and population structure of rice landraces in Guizhou has therefore become a topic of great research interest. However, the influence of ethnic minorities and their traditional food cultures on rice landraces remains unclear. We analyzed the genetic diversity of 598 rice landraces using simple sequence repeat (SSR) markers. Furthermore, we analyzed the nucleotide variations between two similar populations collected during two different time periods using a single-nucleotide polymorphism (SNP) haplotype analysis of six unlinked nuclear loci. The three major results were as follows: (1) The genetic diversity index of rice landraces in six ecologically distinct rice farming zones of Guizhou Province was high (He = 0.7721), and Southwest Guizhou, which has a large population of ethnic minorities, is the center of genetic diversity of rice landraces in the province; this region had the highest He at 0.7823 and the highest polymorphic information content (PIC) at 0.7562. (2) A neighbor-joining (NJ) phylogenetic tree and a model of the population structure showed that the rice landraces from the southwest, south, and southeast of Guizhou had unique genetic structures and genetic backgrounds, which are closely related to the traditional diet cultures of the local ethnic minorities. (3) A nucleotide variation analysis of similar rice landraces collected in 1980 and 2015 revealed that, after 35 years of domestication by ethnic minorities, the original dominant haplotypes were well-preserved; the frequency of the most favorable haplotypes gradually increased to adapt to the traditional food culture. This study is expected to promote the protection and sustainable utilization of rice landraces from this unique region and to provide valuable germplasm materials and information for future rice breeding and basic research efforts. [ABSTRACT FROM AUTHOR]