Status and factors influencing on-farm conservation of Kam Sweet Rice (Oryza sativa L.) genetic resources in southeast Guizhou Province, China

Effects of hormone concentrations on anther cultures and the acquisition of regenerated plants of five awnless triticale genotypes

BACKGROUND

The rapid production of doubled haploids by anther culture technology is an important breeding method for awnless triticale. The aim of this study was to explore the effects of triticale genotype and the types and ratios of exogenous hormones in the medium on the efficiency of triticale anther culture.

RESULTS

Anthers of five triticale genotypes were cultured on four different callus induction media and the calli were induced to differentiate into green plants by culture on three different differentiation media. The triticale genotype T8004 showed the best performance in anther culture, with a callus induction rate of 28.64%, a green plantlet differentiation frequency of 33.33%, and a green plantlet production rate of 2.78%. The highest callus induction rates were obtained by culturing anthers on C3 medium (the main components were potassium nitrate, glutamine, inositol, etc.), and the highest green plantlet differentiation frequency was obtained by culturing calli on D2 differentiation medium (the main components were potassium nitrate, ammonium nitrate, calcium chloride dihydrate, etc.). Flow cytometry analyses showed that 15 of the 20 DH0 generation plants that grew normally in the field were doubled haploids. The average chromosome doubling success rate was 55.6%. Analyses of agronomic traits showed that the 11 DH1 doubled haploid plants reached the standard for awnless triticale, so they are candidate materials for breeding new awnless triticale varieties.

CONCLUSION

The anther culture technology of triticale was optimized in this paper, which made it possible to rapidly breed homozygous varieties of awnless triticale.

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.

Characteristics of antioxidant capacity and metabolomics analysis of flavonoids in the bran layer of green glutinous rice (Oryza sativa L. var. Glutinosa Matsum)

Green glutinous rice is a unique genetic germplasm that has yet to be adequately studied. This study investigated antioxidant capacity and flavonoid metabolites in the bran layer of green glutinous rice (LvH) compared to purple (HeiH), red (HongH) and white (GJG) varieties. The results showed that LvH bran had significantly higher content of total flavonoids and anthocyanin than that of HongH (1.91-fold and 4.34-fold) and GJG (2.45-fold and 13.30-fold). LvH bran also showed significantly higher levels of vitamin B1 and vitamin E than that of HeiH (1.94-fold and 1.15-fold) and HongH (1.22-fold and 1.13-fold), indicating that green glutinous rice bran was rich in bioactive components. LvH bran showed significantly lower IC50 values for scavenging DPPH and ATBS radicals than GJG and even significantly lower IC50 value for scavenging DPPH radicals than HongH, highlighting its potential as an effective source of antioxidants. LvH bran had significantly different downstream metabolite synthesis in the flavonoid pathway compared to HeiH, HongH, and GJG, with 40, 26, and 22 different metabolites, 23, 20, and 33 up-regulated differentially expressed metabolites (DEMs), and 73, 50, and 13 down-regulated DEMs, respectively. Of the 139 flavonoid metabolites identified in colored rice bran, 26 metabolites showed significant positive correlation with both ABTS and DPPH radical scavenging capacity. Typically, quercetin derivatives showed potential for evaluating the antioxidant capacity of colored rice bran. These findings offer valuable insights into the antioxidant properties of green glutinous rice bran and provide references for better understanding of flavonoid metabolites in different colored rice bran.

Transcriptomic profiling of the cold stress and recovery responsiveness of two contrasting Guizhou HE rice genotypes

BACKGROUND

At the seed germination stage, rice is sensitive to cold stress, which adversely affects its growth and development. Guizhou HE rice comprises several different landraces, most of which are cold tolerant.

OBJECTIVE

To identify differentially expressed genes and molecular mechanism underlying the cold tolerance of Guizhou HE.

METHODS

Two Guizhou HE genotypes, AC44 (cold-sensitive) and AC96 (cold-tolerant), which exhibit opposite phenotypes in response to cold treatment at the seed germination stage were used. Comprehensive gene expressions of AC44 and AC96 under 4 °C cold treatment and subsequent recovery conditions were comparatively analyzed by RNA sequencing.

RESULTS

Overall, 11,082 and 7749 differentially expressed genes were detected in AC44 and AC96, respectively. Comparative transcriptome analysis demonstrated that, compared with AC44, AC96 presented fewer upregulated and downregulated genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses demonstrated that AC96 presented more upregulated GO terms, especially terms associated with biological processes. However, AC44 presented more terms related to cellular components, mainly chloroplasts. Moreover, DEGs related to the auxin signaling pathway (including ARF and IAA family members) and transcription factors (including members of the F-box, bZIP, basic helix-loop-helix [bHLH], and MYB-like transcription factor families) were found to be expressed specifically in AC96; thus, these DEGs may be responsible for the cold tolerance of AC96.

CONCLUSIONS

These findings present information about the cold tolerance mechanism of Guizhou HE rice at the germination stage, providing valuable resources and candidate genes for breeding cold-tolerant rice genotypes.

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

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.

Traditional agricultural management of Kam Sweet Rice (Oryza sativa L.) in southeast Guizhou Province, China

BACKGROUND

The Dong people mainly live in Hunan, Guangxi and Guizhou provinces, China, with a long history of glutinous rice cultivation, among which Kam Sweet Rice (KSR) is a group of rice landraces that has been domesticated for thousands of years by the Dong people. The core distribution area of KSR is Liping, Congjiang and Rongjiang County of southeast, Guizhou Province. Paddy fields, forests, livestock and cottages have formed a special artificial wetland ecosystem in local area, and the Dong people have also formed a set of traditional farming systems of KSR for variety breeding, field management, and soil and water conservation. However, this traditional agricultural management has not been reported at multiple levels based on landraces, species and ecosystems.

METHODS

Fieldwork was conducted in ten villages in southeast Guizhou from 2019 to 2021. A total of 229 informants were interviewed from the villages. Semi-structured and key informant interviews were administered to collect ethnoecological data on the characteristics and traditional utilization of KSR, traditional farming systems and agricultural management of the Dong people.

RESULTS

(1): A total of 57 KSR landraces were recorded as used by the Dong people in southeast Guizhou. We analyzed the cultural importance index (CII) of all KSRs. KSR with high CII often has a pleasant taste, special biological characteristics of cold resistance, disease and insect resistance and high utilization in the traditional culture of Dong people. (2) There is a clear division of labor between men and women in the breeding, seed retention, field management and grain storage management of different landraces of KSR in Dong communities. In order to resist natural disasters and insect pests, the cultivation of KSR is usually managed by multi-variety mixed planting. These agricultural management modes are the result of Dong people's understanding and adaptation to the local natural geographical environment, as well as the experience and wisdom crystallization of Dong people's long-term practice. (3) The traditional farmland of Dong People is a typical artificial wetland ecosystem that is planted with mixed KSR landraces with rich traditional wisdom. In addition, the economic benefit of the rice-fish-duck symbiotic system was 3.07 times that of hybrid rice alone; therefore, the rice-fish-duck system not only has the function of maintaining soil, water and ecological balance but also improves the income of Dong people.

CONCLUSION

KSR is a special kind of rice that has been domesticated and cultivated by Dong people for thousands of years. Dong people have also formed traditional agriculture dominated by KSR cultivation. The traditional agricultural management of Dong people provides suitable habitats for flora and fauna with biodiversity protection, and convenient conditions for rational utilization and distribution of water resources were also provided. This traditional management mode is of great significance for environmental protection, climate change response, community resource management, sustainable utilization and agricultural transformation in modern society. Therefore, we call for interdisciplinary research in natural and social sciences, in-depth study of the ecological culture of ethnic areas, and sort out treasures conducive to the development of all mankind.

Traditional knowledge of edible plants used as flavoring for fish-grilling in Southeast Guizhou, China

BACKGROUND

The local Dong people in Qiandongnan Prefecture, Guizhou Province, China, with rich biocultural diversity, have developed the traditional rice-duckweed-fish-duck agroecosystem (RDFDA) to support biodiversity conservation and to meet food and cultural needs. However, there is still not much research on traditional ecological knowledge (TEK) in this area. In particular, there is a lack of traditional knowledge of edible plants used by the Dong people as flavoring to grill fish (Cyprinus carpio) collected from RDFDA, which is extremely valuable in their traditional culture. The study focused on documenting plant species used in grilling fish and analyzing the status of its TEK.

METHODS

Twenty-one sampling points of three Dong minority villages in Qiandongnan were selected for the research. The local TEK associated with plant resources for fish-grilling was recorded through free listing and semi-structured interviews. Fidelity level (FL) and ethnoecological importance value (EIV) indicators were designed to determine the socioeconomic influence of TEK. The non-metric multidimensional scaling (NMDS) method was used to evaluate the differentiation of edible plant species distribution in dissimilar accessibility types.

RESULTS

A total of 430 people were interviewed about grilled fish, of whom 75% were men and 85% were farmers. Thirty-four edible plants were documented for fish-grilling in three Dong villages. They belong to 16 plant families, such as Apiaceae, and Asteraceae. The life forms included herbaceous (76%), shrubs (18%) and trees (6%). Leaves are the most commonly used part of for grilling fish, followed by aerial parts, and whole plants. Among these edible plants, Allium hookeri, A. macrostemon and Houttuynia cordata with the highest fidelity level (100%) were cited as edible plants for grilling fish by all informants. The NMDS showed different accessibility types of collection sites, with different importance values. Paddy rice field edge (2.03) has the highest value, followed by forest-farming ecotone (1.74), streamsides (1.71) and woodland (0.48).

CONCLUSION

The purpose of this study was to investigate the traditional knowledge of edible plant materials used by the Dong people for grilling fish. The results demonstrate the strong connection between local people, the bio-environment and agroecosystem services. The survey and comparative analysis revealed that plant species with high FL values may be potential sources of natural flavors.

Kam Sweet Rice (Oryza sativa L.) Is a Special Ecotypic Rice in Southeast Guizhou, China as Revealed by Genetic Diversity Analysis

Kam Sweet Rice (KSR) is a special kind of rice landrace that has been domesticated for thousands of years by the local Dong people in southeast Guizhou province, China. KSR has many distinguishing characteristics including strong fragrance; high resistance to diseases, pests, and adverse abiotic conditions; difficulty of threshing; and glutinous texture. There is a lack of systematic research on its genetic diversity. In this study, we analyzed the levels and patterns of genetic diversity and nucleotide variation in 1,481 rice germplasm using simple sequence repeat (SSR) markers and single nucleotide polymorphism (SNP) haplotype analysis of six unlinked nuclear loci. The accessions included 315 KSR resources from southeast Guizhou, 578 rice landraces from six rice-growing ecological zones in Guizhou, 546 rice landraces from nine provinces around Guizhou, and 42 wild rice sources. Genetic diversity and heterozygosity of KSR were both low, and thus KSR might be close to a pure rice line. Population structure analysis showed that KSR was isolated into a single type of rice, which had a large genetic distance and a unique genetic background compared to the local varieties in Guizhou province, indicating that KSR is a special rice ecotype. Haplotype analysis of the target genes showed that the population of KSR was rich in haplotypes for resistance to bacterial blight (Xa23) and rice blast (Pid3), and identified unique haplotypes that were different from those of the six rice ecotypes in Guizhou. This study shows that KSR is an excellent rice germplasm resource, provides important information for the improvement and utilization of rice landraces, and serves as a reference for formulating effective rice conservation measures.

Crop genetic erosion: understanding and responding to loss of crop diversity

Crop diversity underpins the productivity, resilience and adaptive capacity of agriculture. Loss of this diversity, termed crop genetic erosion, is therefore concerning. While alarms regarding evident declines in crop diversity have been raised for over a century, the magnitude, trajectory, drivers and significance of these losses remain insufficiently understood. We outline the various definitions, measurements, scales and sources of information on crop genetic erosion. We then provide a synthesis of evidence regarding changes in the diversity of traditional crop landraces on farms, modern crop cultivars in agriculture, crop wild relatives in their natural habitats and crop genetic resources held in conservation repositories. This evidence indicates that marked losses, but also maintenance and increases in diversity, have occurred in all these contexts, the extent depending on species, taxonomic and geographic scale, and region, as well as analytical approach. We discuss steps needed to further advance knowledge around the agricultural and societal significance, as well as conservation implications, of crop genetic erosion. Finally, we propose actions to mitigate, stem and reverse further losses of crop diversity.

Edible Plant Oil: Global Status, Health Issues, and Perspectives

Edible plant oil (EPO) is an indispensable nutritional resource for human health. Various cultivars of oil-bearing plants are grown worldwide, and the chemical compositions of different plant oils are diverse. The extremely complex components in oils lead to diverse standards for evaluating the quality and safety of different EPOs. The environment poses great challenges to the EPO safety and quality during the entire industrial chain, including plant cultivation, harvesting, oil processing, and storage. Environmental risk factors include heavy metal or pesticide residue pollution, insect or harmful microbial infestation, and rancidity. Here, the diverse components in oil and various oil-producing processes are discussed, including plant species, oil yield, and composition complexity, environmental factors that degrade oil quality. Additionally, we propose a whole-industrial-chain monitoring system instead of current single-link-monitoring approach by monitoring and tracking the quality and safety of EPOs during the entire process of plant cultivation, raw materials harvest, oil process, and EPOs storage. This will provide guidance for monitoring the quality and safety of EPOs, which were challenged by the deteriorating environment.