Genomic footprints of Kam Sweet Rice domestication indicate possible migration routes of the Dong people in China and provide resources for future rice breeding

Large-scale genomic and phenomic analyses of modern cultivars empower future rice breeding design

Modern cultivated rice plays a pivotal role in global food security. China accounts for nearly 30% of the world's rice production and has developed numerous cultivated varieties over the past decades that are well adapted to diverse growing regions. However, the genomic bases underlying the phenotypes of these modern cultivars remain poorly characterized, limiting the exploitation of this vast resource for breeding specialized, regionally adapted cultivars. In this study, we constructed a comprehensive genetic variation map of modern rice using resequencing datasets from 6044 representative cultivars from five major rice-growing regions in China. Our genomic and phenotypic analyses of this diversity panel revealed regional preferences for specific genomic backgrounds and traits, such as heading date, biotic/abiotic stress resistance, and grain shape, which are crucial for adaptation to local conditions and consumer preferences. We identified 3131 quantitative trait loci associated with 53 phenotypes across 212 datasets under various environmental conditions through genome-wide association studies. Notably, we cloned and functionally verified a novel gene related to grain length, OsGL3.6. By integrating multiple datasets, we developed RiceAtlas, a versatile multi-scale toolkit for rice breeding design. We successfully utilized the RiceAtlas breeding design function to rapidly improve the grain shape of the Suigeng4 cultivar. These valuable resources enhance our understanding of the adaptability and breeding requirements of modern rice and can facilitate advances in future rice-breeding initiatives.

Linkage Mapping and Identification of Candidate Genes for Cold Tolerance in Rice (Oryza Sativa L.) at the Bud Bursting Stage

Rice is highly sensitive to low temperatures, making cold stress a significant factor limiting its growth, especially during the bud bursting stage. To address this, an RIL population derived from a cross between cold-tolerant and cold-sensitive rice varieties was used to identify nine QTLs linked to cold tolerance under temperatures of 4 ℃, 5 °C, and 6 ℃ using a high-density genetic map. One candidate gene, LOC_Os07g44410, was identified through gene function annotation, haplotype analysis, and qRT-PCR, with two main haplotypes (Hap1 and Hap2) showing distinct phenotypic differences. qRT-PCR analysis showed that the expression level of LOC_Os07g44410 in cold tolerant lines carrying Hap1 was significantly higher than that in cold sensitive lines carrying Hap2. Hap1, associated with greater cold tolerance, was predominant in japonica rice, while Hap2 related to cold sensitive was majority in indica rice. This study offers valuable genetic resources for further research on cold tolerance mechanisms and breeding applications at the bud bursting stage in rice.

Altered expression of amino acid permease OsAAP11 mediates bud outgrowth and tillering by regulating transport and accumulation of amino acids in rice

Kam sweet rice is a cultural treasure in Qiandongnan, Guizhou Province. However, the situation with low yield and economic value in Kam sweet rice urgently requires improved mechanistic understanding of tillering to increase its yield. In this study, we found that the rate of axillary bud elongation differed significantly among Kam sweet rice varieties, which was positively correlated with tiller number. Transcriptome analysis suggests that genes involved in nitrogen metabolism and plant hormone signaling pathways could be the main reasons for the differences in tillering among these varieties. The amino acid transporter OsAAP11 in the transcriptome was essential for bud outgrowth and rice tillering based on the phenotypic performance of its transgenic plants. Further results found that OsAAP11 was able to transport amino acids such as proline, glycine, and alanine in rice. Natural variations were found in the promoter region of this gene in different Kam sweet rice varieties, which may lead to differences in the transcription levels of OsAAP11. Overall, the results suggest that the natural variations of OsAAP11 in rice might lead to variations in its expression levels, further affecting bud outgrowth and tillering through regulating the transport and accumulation of amino acids.

Genetic profile and ancestral polymorphism research of the Guizhou Shui and Dong ethnic groups using a novel self-developed AIM-InDel panel

Insertion or deletion (InDel), a genetic marker with short insertion/deletion fragment length polymorphism, is widely used in the field of forensic biological research. The Guizhou Shui (Shui) ethnic group and Guizhou Dong (Dong) ethnic group are located in the southwestern region of China, with rich historical and cultural background. In this study, a self-developed panel included 56 ancestry informative marker (AIM)-InDel loci on the autosomes, three InDel loci on the Y chromosome, and one sex-determined Amelogenin locus. Firstly, we used the 56 autosomal loci to assess the forensic individual identification and paternity testing abilities in both the Shui and Dong groups. The cumulative probability of match and probability of exclusion for the Shui and Dong groups were 2.228×10-15 and 0.991518139; 7.604×10-16 and 0.992253273, respectively. In addition, we also conducted in-depth analyses for the genetic backgrounds and structures of the Shui and Dong groups based on 56 AIM-InDel loci. This research has found that the Shui and Dong groups have close genetic relationships with the East Asian populations. Meanwhile, we also found that the Shui group has a close genetic distance with Chinese Dai in Xishuangbanna (CDX). These insights provide vital information for the genetic structures of the Shui and Dong groups, as well as basic population data and molecular biological evidence support for individual identification and biogeographic ancestry inference in forensic genetic field.

Linkage Mapping and Discovery of Candidate Genes for Drought Tolerance in Rice During the Vegetative Growth Period

Drought is a major abiotic stress affecting crop yields. Mapping quantitative trait loci (QTLs) and mining genes for drought tolerance in rice are important for identifying gene functions and targets for molecular breeding. Here, we performed linkage analysis of drought tolerance using a recombinant inbred line population derived from Jileng 1 (drought sensitive) and Milyang 23 (drought tolerant). An ultra-high-density genetic map, previously constructed by our research team using genotype data from whole-genome sequencing, was used in combination with phenotypic data for rice grown under drought stress conditions in the field in 2017-2019. Thirty-nine QTLs related to leaf rolling index and leaf withering degree were identified, and QTLs were found on all chromosomes except chromosomes 6, 10, and 11. qLWD4-1 was detected after 32 days and 46 days of drought stress in 2017 and explained 7.07-8.19% of the phenotypic variation. Two loci, qLRI2-2 and qLWD4-2, were identified after 29, 42, and 57 days of drought stress in 2018. These loci explained 10.59-17.04% and 5.14-5.71% of the phenotypic variation, respectively. There were 281 genes within the QTL interval. Through gene functional annotation and expression analysis, two candidate genes, Os04g0574600 and OsCHR731, were found. Quantitative reverse transcription PCR analysis showed that the expression levels of these genes were significantly higher under drought stress than under normal conditions, indicating positive regulation. Notably, Os04g0574600 was a newly discovered drought tolerance gene. Haplotype analysis showed that the RIL population carried two haplotypes (Hap1 and Hap2) of both genes. Lines carrying Hap2 exhibited significantly or extremely stronger drought tolerance than those carrying Hap1, indicating that Hap2 is an excellent haplotype. Among rice germplasm resources, there were two and three haplotypes of Os04g0574600 and OsCHR731, respectively. A high proportion of local rice resources in Sichuan, Yunnan, Anhui, Guangdong and Fujian provinces had Hap of both genes. In wild rice, 50% of accessions contained Hap1 of Os04g0574600 and 50% carried Hap4; 13.51%, 59.46% and 27.03% of wild rice accessions contained Hap1, Hap2, and Hap3, respectively. Hap2 of Os04g0574600 was found in more indica rice resources than in japonica rice. Therefore, Hap2 has more potential for utilization in future drought tolerance breeding of japonica rice.

Photoperiod-Dependent Nutrient Accumulation in Rice Cultivated in Plant Factories: A Comparative Metabolomic Analysis

Plant factories offer a promising solution to some of the challenges facing traditional agriculture, allowing for year-round rapid production of plant-derived foods. However, the effects of conditions in plant factories on metabolic nutrients remain to be explored. In this study, we used three rice accessions (KongYu131, HuangHuaZhan, and Kam Sweet Rice) as objectives, which were planted in a plant factory with strict photoperiods that are long-day (12 h light/12 h dark) or short-day (8 h light/16 h dark). A total of 438 metabolites were detected in the harvested rice grains. The difference in photoperiod leads to a different accumulation of metabolites in rice grains. Most metabolites accumulated significantly higher levels under the short-day condition than the long-day condition. Differentially accumulated metabolites were enriched in the amino acids and vitamin B6 pathway. Asparagine, pyridoxamine, and pyridoxine are key metabolites that accumulate at higher levels in rice grains harvested from the short-day photoperiod. This study reveals the photoperiod-dependent metabolomic differences in rice cultivated in plant factories, especially the metabolic profiling of taste- and nutrition-related compounds.

Ethnobotanical studies on rice landraces under on-farm conservation in Xishuangbanna of Yunnan Province, China

BACKGROUND

A complex interaction and mutual influence exists among landscapes, cultures, and landraces, with rice culture being a typical embodiment of this relationship. The conservation of landraces operates alongside preserving traditional practices. The Xishuangbanna region stands out as a hub for the genetic diversity of landraces, boasting rich genetic resources. Despite the diverse rice resources in this region, a comprehensive and systematic study has not been undertaken.

METHODS

From October to November 2023, we collected rice landraces under the on-farm conservation in 18 townships including Menghai, Mengla and Jinghong in Xishuangbanna. Employing semi-structured interviews and various methods, we investigated factors influencing the preservation and loss of rice landraces in the region. Statistical analysis was applied to the agronomic traits of collected local rice, encompassing indica or japonica, glutinous or non-glutinous, grain shape, and hull color as second category traits. The second category included quantitative traits like thousand grain weight and grain length. Rice diversity among different regions, traits, and ethnic groups was assessed using the Shannon-Wiener index. Additionally, clustering analysis via the UPGMA method depicted the distribution characteristics of the resources.

RESULTS

A total of 70 rice landraces were collected in the Xishuangbanna region, each exhibiting distinct characteristics. Differences were observed across regions, trait, naming, and ethnic groups. Diversity analysis revealed that Mengla had the highest diversity, followed by Menghai, while Jinghong exhibited the lowest diversity. The second category of traits displayed broader diversity than the first, with the Dai people's glutinous rice showcasing greater diversity than other ethnic groups. Cluster analysis categorized the 70 samples into seven groups at a genetic distance of 1.15. Ethnobotanical interviews emphasized the rapid loss of rice landraces resources in Xishuangbanna, with indigenous ethnic cultures playing a vital role in the conservation of rice landraces. Dai traditions, in particular, played a crucial role in protecting glutinous rice resources, showcasing a mutual dependence between Dai culture and glutinous rice.

CONCLUSIONS

The rich natural environment and diverse ethnic cultures in Xishuangbanna have given rise to various rice landraces. The Dai, primary cultivators of glutinous rice with higher diversity, intertwine their traditional ethnic culture with the conservation of glutinous rice resources. At the same time, the preserving glutinous rice resources promotes the inheritance of Dai ethnic culture. However, rice landraces are facing the risk of loss. Hence, collecting and documenting rice landraces is crucial. Encourage local communities to sustain and expand their cultivation, promoting on-farm conservation. These measures contribute valuable germplasm and genes for rice breeding and serve as a means of cultural preservation.

Blocking of awn development-related gene OsGAD1 coordinately boosts yield and quality of Kam Sweet Rice

Kam Sweet Rice is a high-quality local variety of Guizhou province in China, but most varieties have awns on lemma. In this study, we aimed to obtain awnless varieties of Kam Sweet Rice by blocking the awn development-related gene OsGAD1 using CRISPR/Cas9 technology. We determined that natural variations of the OsGAD1 triggered different lengths of awns of Kam Sweet Rice. We found that the awning rate of the CRISPR lines of OsGAD1 in Guxiangnuo, Goujingao and Gouhuanggang decreased by over 65%, and the number of grains per panicle and yield per plant increased by more than 17% and 20% compared to the wild-types. Furthermore, we indicated that blocking OsGAD1 resulted in an increase of over 2% in the brown rice rate and milled rice rate in these varieties. In addition, the analysis of the transcriptome revealed that the regulation of awn development and yield formation in CRISPR lines of OsGAD1 may involve genes associated with phytohormone and nitrogen pathways. These results suggest that blocking OsGAD1 in Kam Sweet Rice using CRISPR/Cas9 technology can be used for breeding programs seeking high yield and grain quality of Kam Sweet Rice.