A wild rice CSSL population facilitated identification of salt tolerance genes and rice germplasm innovation.

Salt stress is one of the major factors that limits rice production. Therefore, identification of salt-tolerant alleles from wild rice is important for rice breeding. In this study, we constructed a set of chromosome segment substitution lines (CSSLs) using wild rice as the donor parent and cultivated rice Nipponbare (Nip) as the recurrent parent. Salt tolerance germinability (STG) was evaluated, and its association with genotypes was determined using this CSSL population. We identified 17 QTLs related to STG. By integrating the transcriptome and genome data, four candidate genes were identified, including the previously reported AGO2 and WRKY53. Compared with Nip, wild rice AGO2 has a structure variation in its promoter region and the expression levels were upregulated under salt treatments; wild rice WRKY53 also has natural variation in its promoter region, and the expression levels were downregulated under salt treatments. Wild rice AGO2 and WRKY53 alleles have combined effects for improving salt tolerance at the germination stage. One CSSL line, CSSL118 that harbors these two alleles was selected. Compared with the background parent Nip, CSSL118 showed comprehensive salt tolerance and higher yield, with improved transcript levels of reactive oxygen species scavenging genes. Our results provided promising genes and germplasm resources for future rice salt tolerance breeding.

A functional chromogen gene C from wild rice is involved in a different anthocyanin biosynthesis pathway in indica and japonica.

KEY MESSAGE: we identified a functional chromogen gene C from wild rice, providing a new insight of anthocyanin biosynthesis pathway in indica and japonica. Accumulation of anthocyanin is a desirable trait to be selected in rice domestication, but the molecular mechanism of anthocyanin biosynthesis in rice remains largely unknown. In this study, a novel allele of chromogen gene C, OrC1, from Oryza rufipongon was cloned and identified as a determinant regulator of anthocyanin biosynthesis. Although OrC1 functions in purple apiculus, leaf sheath and stigma in indica background, it only promotes purple apiculus in japonica. Transcriptome analysis revealed that OrC1 regulates flavonoid biosynthesis pathway and activates a few bHLH and WD40 genes of ternary MYB-bHLH-WD40 complex in indica. Differentially expressed genes and metabolites were found in the indica and japonica backgrounds, indicating that OrC1 activated the anthocyanin biosynthetic genes OsCHI, OsF3H and OsANS and produced six metabolites independently. Artificial selection and domestication of C1 gene in rice occurred on the coding region in the two subspecies independently. Our results reveal the regulatory system and domestication of C1, provide new insights into MYB transcript factor involved in anthocyanin biosynthesis, and show the potential of engineering anthocyanin biosynthesis in rice.

Identification and genetic analysis of qCL1.2, a novel allele of the "green revolution" gene SD1 from wild rice (Oryza rufipogon) that enhances plant height.

BACKGROUND: The exploitation of novel alleles from wild rice that were lost during rice cultivation could be very important for rice breeding and evolutionary studies. Plant height (PH) was a target of artificial selection during rice domestication and is still a target of modern breeding. The "green revolution" gene semi-dwarf 1 (SD1) were well documented and used in the past decades, allele from wild rice could provide new insights into the functions and evolution of this gene. RESULTS: We identified a PH-related quantitative trait locus, qCL1.2,from wild riceusing a set of chromosome segment substitution lines. qCL1.2encodesa novel allele of SD1 gene. The wild allele of SD1 is a dominant locus that can significantly promote rice internode length by regulating the expression levels of genes involved in gibberellin biosynthesis and signal transduction. Nucleotide diversity and haplotype network analyses of the SD1 gene were performed using 2822 rice landraces. Two previously reported functional nucleotide polymorphisms clearly differentiated japonica and indica rice; however, they were not associated with PH selection. Other new functional nucleotide polymorphisms in the coding, but not promoter, regions were involved in PH selection during rice domestication. Our study increasesunderstanding of the rice SD1 gene and provides additional evidence of this gene's selection during rice domestication. CONCLUSIONS: Our findings provide evidence thatSD1 gene from wild rice enhances plant height and new functional nucleotide polymorphisms of this gene were artificially selected during cultivated rice differentiation.

Haplotype-resolved gapless genome and chromosome segment substitution lines facilitate gene identification in wild rice.

The abundant genetic variation harbored by wild rice (Oryza rufipogon) has provided a reservoir of useful genes for rice breeding. However, the genome of wild rice has not yet been comprehensively assessed. Here, we report the haplotype-resolved gapless genome assembly and annotation of wild rice Y476. In addition, we develop two sets of chromosome segment substitution lines (CSSLs) using Y476 as the donor parent and cultivated rice as the recurrent parents. By analyzing the gapless reference genome and CSSL population, we identify 254 QTLs associated with agronomic traits, biotic and abiotic stresses. We clone a receptor-like kinase gene associated with rice blast resistance and confirm its wild rice allele improves rice blast resistance. Collectively, our study provides a haplotype-resolved gapless reference genome and demonstrates a highly efficient platform for gene identification from wild rice.

Global whole-genome comparison and analysis to classify subpopulations and identify resistance genes in weedy rice relevant for improving crops.

Common weedy rice plants are important genetic resources for modern breeding programs because they are the closest relatives to rice cultivars and their genomes contain elite genes. Determining the utility and copy numbers of WRKY and nucleotide-binding site (NBS) resistance-related genes may help to clarify their variation patterns and lead to crop improvements. In this study, the weedy rice line LM8 was examined at the whole-genome level. To identify the Oryza sativa japonica subpopulation that LM8 belongs to, the single nucleotide polymorphisms (SNPs) of 180 cultivated and 23 weedy rice varieties were used to construct a phylogenetic tree and a principal component analysis and STRUCTURE analysis were performed. The results indicated that LM8 with admixture components from japonica (GJ) and indica (XI) belonged to GJ-admixture (GJ-adm), with more than 60% of its genetic background derived from XI-2 (22.98%), GJ-tropical (22.86%), and GJ-subtropical (17.76%). Less than 9% of its genetic background was introgressed from weedy rice. Our results also suggested LM8 may have originated in a subtropical or tropical geographic region. Moreover, the comparisons with Nipponbare (NIP) and Shuhui498 (R498) revealed many specific structure variations (SVs) in the LM8 genome and fewer SVs between LM8 and NIP than between LM8 and R498. Next, 96 WRKY and 464 NBS genes were identified and mapped on LM8 chromosomes to eliminate redundancies. Three WRKY genes (ORUFILM02g002693, ORUFILM05g002725, and ORUFILM05g001757) in group III and one RNL [including the resistance to powdery mildew 8 (RPW8) domain, NBS, and leucine rich repeats (LRRs)] type NBS gene (ORUFILM12g000772) were detected in LM8. Among the NBS genes, the RPW8 domain was detected only in ORUFILM12g000772. This gene may improve plant resistance to pathogens as previously reported. Its classification and potential utility imply LM8 should be considered as a germplasm resource relevant for rice breeding programs.

LncPheDB: a genome-wide lncRNAs regulated phenotypes database in plants.

LncPheDB (https://www.lncphedb.com/) is a systematic resource of genome-wide long non-coding RNAs (lncRNAs)-phenotypes associations for multiple species. It was established to display the genome-wide lncRNA annotations, target genes prediction, variant-trait associations, gene-phenotype correlations, lncRNA-phenotype correlations, and the similar non-coding regions of the queried sequence in multiple species. LncPheDB sorted out a total of 203,391 lncRNA sequences, 2000 phenotypes, and 120,271 variants of nine species (Zea mays L., Gossypium barbadense L., Triticum aestivum L., Lycopersicon esculentum Mille, Oryza sativa L., Hordeum vulgare L., Sorghum bicolor L., Glycine max L., and Cucumis sativus L.). By exploring the relationship between lncRNAs and the genomic position of variants in genome-wide association analysis, a total of 68,862 lncRNAs were found to be related to the diversity of agronomic traits. More importantly, to facilitate the study of the functions of lncRNAs, we analyzed the possible target genes of lncRNAs, constructed a blast tool for performing similar fragmentation studies in all species, linked the pages of phenotypic studies related to lncRNAs that possess similar fragments and constructed their regulatory networks. In addition, LncPheDB also provides a user-friendly interface, a genome visualization platform, and multi-level and multi-modal convenient data search engine. We believe that LncPheDB plays a crucial role in mining lncRNA-related plant data. Supplementary Information: The online version contains supplementary material available at 10.1007/s42994-022-00084-3.

Genomic Analysis Provides Insights Into the Plant Architecture Variations in in situ Conserved Chinese Wild Rice (Oryza rufipogon Griff.).

In situ conserved wild rice (Oryza rufipogon Griff.) is a promising source of alleles for improving rice production worldwide. In this study, we conducted a genomic analysis of an in situ conserved wild rice population (Guiping wild rice) growing at the center of wild rice genetic diversity in South China. Differences in the plant architecture in this population were investigated. An analysis using molecular markers revealed the substantial genetic diversity in this population, which was divided into subgroups according to the plant architecture. After resequencing representative individuals, the Guiping wild rice population was compared with other O. rufipogon and Oryza sativa populations. The results indicated that this in situ conserved wild rice population has a unique genetic structure, with genes that were introgressed from aromatic and O. sativa ssp. indica and japonica populations. The QTLs associated with plant architecture in this population were detected via a pair-wise comparison analysis of the sequencing data for multiple DNA pools. The results suggested that a heading date-related gene (DHD1) might be associated with variations in plant architecture and may have originated in cultivated rice. Our findings provide researchers with useful insights for future genomic analyses of in situ conserved wild rice populations.

Identification of candidate genes and clarification of the maintenance of the green pericarp of weedy rice grains.

The weedy rice (Oryza sativa f. spontanea) pericarp has diverse colors (e.g., purple, red, light-red, and white). However, research on pericarp colors has focused on red and purple, but not green. Unlike many other common weedy rice resources, LM8 has a green pericarp at maturity. In this study, the coloration of the LM8 pericarp was evaluated at the cellular and genetic levels. First, an examination of their ultrastructure indicated that LM8 chloroplasts were normal regarding plastid development and they contained many plastoglobules from the early immature stage to maturity. Analyses of transcriptome profiles and differentially expressed genes revealed that most chlorophyll (Chl) degradation-related genes in LM8 were expressed at lower levels than Chl a/b cycle-related genes in mature pericarps, suggesting that the green LM8 pericarp was associated with inhibited Chl degradation in intact chloroplasts. Second, the F2 generation derived from a cross between LM8 (green pericarp) and SLG (white pericarp) had a pericarp color segregation ratio of 9:3:4 (green:brown:white). The bulked segregant analysis of the F2 populations resulted in the identification of 12 known genes in the chromosome 3 and 4 hotspot regions as candidate genes related to Chl metabolism in the rice pericarp. The RNA-seq and sqRT-PCR assays indicated that the expression of the Chl a/b cycle-related structural gene DVR (encoding divinyl reductase) was sharply up-regulated. Moreover, genes encoding magnesium-chelatase subunit D and the light-harvesting Chl a/b-binding protein were transcriptionally active in the fully ripened dry pericarp. Regarding the ethylene signal transduction pathway, the CTR (encoding an ethylene-responsive protein kinase) and ERF (encoding an ethylene-responsive factor) genes expression profiles were determined. The findings of this study highlight the regulatory roles of Chl biosynthesis- and degradation-related genes influencing Chl accumulation during the maturation of the LM8 pericarp.

Genome-wide selection and introgression of Chinese rice varieties during breeding.

China is the largest rice-producing country, but the genomic landscape of rice diversity has not yet been clarified. In this study, we re-sequence 1070 rice varieties collected from China (400) and other regions in Asia (670). Among the six major rice groups (aus, indica-I, indica-II, aromatic, temperate japonica, and tropical japonica), almost all Chinese varieties belong to the indica-II or temperate japonica group. Most Chinese indica varieties belong to indica-II, which consists of two subgroups developed during different phases of rice breeding. The genomic segments underlying the differences between these subgroups span 36.32 Mb. The Chinese japonica rice varieties fall into the temperate japonica group, consisting of two subgroups based on their geographical distribution. The genomic segments underlying the differences between these subgroups span 27.69 Mb. These differentiated segments in the Chinese indica varieties span 45 genes with nonsynonymous mutations that are closely related to variations in plant height and grain width. Fifty-four genes with nonsynonymous mutations are associated with the differences in heading date between the two Chinese japonica subgroups. These findings provide new insights into rice diversity in China that will facilitate the molecular breeding.