Whole-genome analysis revealed the positively selected genes during the differentiation of indica and temperate japonica rice

The ties of brotherhood between japonica and indica rice for regional adaptation

Selection of beneficial genomic variants was crucial for regional adaptation of crops during domestication, but the underlying genomic basis remains largely unexplored. Here we report a genome-wide selective-sweep analysis of 655 japonica and 1,205 indica accessions selected from 2,673 landraces through principal component analysis to identify 5,636 non-synonymous single nucleotide polymorphisms (SNPs) fixed in at least one subspecies. We classified these SNPs into three groups, jiS (japonica- and indica-selected), jS (japonica-selected only), and iS (indica-selected only), and documented evidence for selection acting on these groups, their relation to yield-related traits, such as heading date, and their practical value in cropping area prediction. We also demonstrated the role of a jiS-SNP-containing gene in temperature adaptability. Our study informs genes underpinning adaptation that may shape Green Super Rice and proposes a time-saving, cost-reducing selection strategy of genomic breeding, sweep-SNP-guided selection, for developing regionally-adapted heterosis.

High-Quality Genomes and High-Density Genetic Map Facilitate the Identification of Genes From a Weedy Rice

Genes have been lost or weakened from cultivated rice during rice domestication and breeding. Weedy rice (Oryza sativa f. spontanea) is usually recognized as the progeny between cultivated rice and wild rice and is also known to harbor an gene pool for rice breeding. Therefore, identifying genes from weedy rice germplasms is an important way to break the bottleneck of rice breeding. To discover genes from weedy rice germplasms, we constructed a genetic map based on w-hole-genome sequencing of a F₂ population derived from the cross between LM8 and a cultivated rice variety. We further identified 31 QTLs associated with 12 important agronomic traits and revealed that ORUFILM03g000095 gene may play an important role in grain length regulation and participate in grain formation. To clarify the genomic characteristics from weedy rice germplasms of LM8, we generated a high-quality genome assembly using single-molecule sequencing, Bionano optical mapping, and Hi-C technologies. The genome harbored a total size of 375.8 Mb, a scaffold N50 of 24.1 Mb, and originated approximately 0.32 million years ago (Mya) and was more closely related to Oryza sativa ssp. japonica. and contained 672 unique genes. It is related to the formation of grain shape, heading date and tillering. This study generated a high-quality reference genome of weedy rice and high-density genetic map that would benefit the analysis of genome evolution for related species and suggested an effective way to identify genes related to important agronomic traits for further rice breeding.

Genome-Wide Association Mapping to Identify Genetic Loci for Cold Tolerance and Cold Recovery During Germination in Rice

Low temperature significantly affects rice growth and yield. Temperatures lower than 15°C are generally detrimental for germination and uniform seedling stand. To investigate the genetic architecture underlying cold tolerance during germination in rice, we conducted a genome-wide association study using a novel diversity panel of 257 rice accessions from around the world and the 7K SNP marker array. Phenotyping was conducted in controlled growth chambers under dark conditions at 13°C. The rice accessions were measured for low-temperature germinability, germination index, coleoptile length under cold stress, plumule length at 4-day recovery, and plumule length recovery rate. A total of 51 QTLs were identified at p < 0.001 and 17 QTLs were identified using an FDR < 0.05 across the different chilling indices with the whole panel of accessions. At the threshold of p < 0.001, a total of 20 QTLs were identified in the subset of japonica accessions, while 9 QTLs were identified in the subset of indica accessions. Considering the recurring SNPs and linked SNPs across different chilling indices, we identified 31 distinct QTL regions in the whole panel, 13 QTL regions in the japonica subset, and 7 distinct QTL regions in the indica subset. Among these QTL regions, three regions were common between the whole panel and japonica, three regions were common between the whole panel and indica, and one region was common between indica and japonica. A subset of QTL regions was potentially colocalized with previously identified genes and QTLs, including 10 from the japonica subset, 4 from the indica subset, and 6 from the whole panel. On the other hand, a total of 21 potentially novel QTL regions from the whole panel, 10 from the japonica subset, and 1 from the indica subset were identified. The results of our study provide useful information on the genetic architecture underlying cold tolerance during germination in rice, which in turn can be used for further molecular study and crop improvement for low-temperature stressed environments.

Discovery of Functional SNPs via Genome-Wide Exploration of Malaysian Pigmented Rice Varieties

Recently, rice breeding program has shown increased interests on the pigmented rice varieties due to their benefits to human health. However, the genetic variation of pigmented rice varieties is still scarce and remains unexplored. Hence, we performed genome-wide SNP analysis from the genome resequencing of four Malaysian pigmented rice varieties, representing two black and two red rice varieties. The genome of four pigmented varieties was mapped against Nipponbare reference genome sequences, and 1.9 million SNPs were discovered. Of these, 622 SNPs with polymorphic sites were identified in 258 protein-coding genes related to metabolism, stress response, and transporter. Comparative analysis of 622 SNPs with polymorphic sites against six rice SNP datasets from the Ensembl Plants variation database was performed, and 70 SNPs were identified as novel SNPs. Analysis of SNPs in the flavonoid biosynthetic genes revealed 40 nonsynonymous SNPs, which has potential as molecular markers for rice seed colour identification. The highlighted SNPs in this study show effort in producing valuable genomic resources for application in the rice breeding program, towards the genetic improvement of new and improved pigmented rice varieties.

Global Transcriptome and Co-Expression Network Analysis Reveal Contrasting Response of Japonica and Indica Rice Cultivar to γ Radiation

Japonica and indica are two important subspecies in cultivated Asian rice. Irradiation is a classical approach to induce mutations and create novel germplasm. However, little is known about the differential response between japonica and indica rice after γ radiation. Here, we utilized the RNA sequencing and Weighted Gene Co-expression Network Analysis (WGCNA) to compare the transcriptome differences between japonica Nipponbare (NPB) and indica Yangdao6 (YD6) in response to irradiation. Japonica subspecies are more sensitive to irradiation than the indica subspecies. Indica showed a higher seedling survival rate than japonica. Irradiation caused more extensive DNA damage in shoots than in roots, and the severity was higher in NPB than in YD6. GO and KEGG pathway analyses indicate that the core genes related to DNA repair and replication and cell proliferation are similarly regulated between the varieties, however the universal stress responsive genes show contrasting differential response patterns in japonica and indica. WGCNA identifies 37 co-expressing gene modules and ten candidate hub genes for each module. This provides novel evidence indicating that certain peripheral pathways may dominate the molecular networks in irradiation survival and suggests more potential target genes in breeding for universal stress tolerance in rice.

Selective sweep with significant positive selection serves as the driving force for the differentiation of japonica and indica rice cultivars

BACKGROUND

Asian cultivated rice (Oryza sativa L.), including japonica and indica, is unarguable the most important crop in Asia as well as worldwide. However, a decisive conclusion of its origination and domestication processes are still lacking. Nowadays, the ever-increasing high-throughput sequencing data of numerous rice samples have provided us new opportunities to get close to the answer of these questions.

RESULTS

By compiling 296 whole-genome sequenced rice cultivars and 39 diverse wild rice, two types of domesticated regions (DR-I and DR-II) with strong selective sweep signals between different groups were detected. DR-I regions included 28 blocks which significantly differentiated between japonica and indica subspecies, while DR-II regions were consisted of another 28 blocks which significantly differentiated between wild and cultivated rice, each covered 890 kb and 640 kb, respectively. In-depth analysis suggested that both DR-Is and DR-IIs could have originated from Indo-China Peninsula to southern China, and DR-IIs might be introgressed from indica to japonica. Functional bias with significant positive selection has also been detected in the genes of DR-I, suggesting important role of the selective sweep in differentiation of japonica and indica.

CONCLUSIONS

This research promoted a new possible model of the origin of the cultivated rice that DR-Is in japonica and indica maybe independently originated from the divergent wild rice in the Indo-China Peninsula to southern China, and then followed by frequent introgression. Genes with significant positive selection and biased functions were also detected which could play important roles in rice domestication and differentiation processes.

Candidate loci involved in domestication and improvement detected by a published 90K wheat SNP array

Selection is one of the most important forces in crop evolution. Common wheat is a major world food crop and a typical allopolyploid with a huge and complex genome. We applied four approaches to detect loci selected in wheat during domestication and improvement. A total of 7,984 candidate loci were detected, accounting for 23.3% of all 34,317 SNPs analysed, a much higher proportion than estimated in previous reports. We constructed a first generation wheat selection map which revealed the following new insights on genome-wide selection: (1) diversifying selection acted by increasing, decreasing or not affecting gene frequencies; (2) the number of loci under selection during domestication was much higher than that during improvement; (3) the contribution to wheat improvement by the D sub-genome was relatively small due to the bottleneck of hexaploidisation and diversity can be expanded by using synthetic wheat and introgression lines; and (4) clustered selection regions occur throughout the wheat genome, including the centromere regions. This study will not only help future wheat breeding and evolutionary studies, but will also accelerate study of other crops, especially polyploids.

New Genetic Loci Associated with Preharvest Sprouting and Its Evaluation Based on the Model Equation in Rice

Preharvest sprouting (PHS) in rice panicles is an important quantitative trait that causes both yield losses and the deterioration of grain quality under unpredictable moisture conditions at the ripening stage. However, the molecular mechanism underlying PHS has not yet been elucidated. Here, we explored the genetic loci associated with PHS in rice and formulated a model regression equation for rapid screening for use in breeding programs. After re-sequencing 21 representative accessions for PHS and performing enrichment analysis, we found that approximately 20,000 SNPs revealed distinct allelic distributions between PHS resistant and susceptible accessions. Of these, 39 candidate SNP loci were selected, including previously reported QTLs. We analyzed the genotypes of 144 rice accessions to determine the association between PHS and the 39 candidate SNP loci, 10 of which were identified as significantly affecting PHS based on allele type. Based on the allele types of the SNP loci, we constructed a regression equation for evaluating PHS, accounting for an R² value of 0.401 in japonica rice. We validated this equation using additional accessions, which exhibited a significant R² value of 0.430 between the predicted values and actual measurements. The newly detected SNP loci and the model equation could facilitate marker-assisted selection to predict PHS in rice germplasm and breeding lines.