Construction of Near Isogenic Lines for Pericarp Color and Evaluation on Their Near isogenicity in Rice

The inheritance of purple pericarp was studied through genetic analysis using F2, BC1F1 and F3 from a cross between a purple pericarp rice variety Zixiangnuo and a white pericarp rice variety Chunjiangnuo 2. Seven pairs of near isogenic lines （NILs） for pericarp color of rice were further constructed. Genetic analysis indicated that the purple pericarp was controlled by two complementary genes （Pb and Pp）. Agronomic trait analysis and polymorphism analysis using SSR markers on these seven pairs of NILs were used in the evaluation of near-isogenicity. No significant differences in agronomic traits were found except 1000-grain weight between the NILs. The polymorphic SSR markers for the parents were only detected in target segments of the five pairs of NILs different in Pb, which revealed the ideal near isogenicity of them. However, for the two pairs of NILs different in Pp, the polymorphic markers for the two parents were detected as well as in non-targeted segments of chromosomes 11 and 12, respectively.

Population genomic analysis unravels the evolutionary roadmap of pericarp color in rice

Pigmented rice stands out for its nutritional value and is gaining more and more attention.Wild rice,domes-ticated red rice,and weedy rice all have a red pericarp and a comprehensive genetic background in terms of the red-pericarp phenotype.We performed population genetic analyses using 5104 worldwide rice acces-sions,including 2794 accessions with red or black pericarps,85 of which were newly sequenced in this study.The results suggested an evolutionary trajectory of red landraces originating from wild rice,and the split times of cultivated red and white rice populations were estimated to be within the past 3500 years.Cultivated red rice was found to feralize to weedy rice,and weedy rice could be further re-domesticated to cultivated red rice.A genome-wide association study based on the 2794 accessions with pigmented peri-carps revealed several new candidate genes associated with the red-pericarp trait for further functional characterization.Our results provide genomic evidence for the origin of pigmented rice and a valuable genomic resource for genetic investigation and breeding of pigmented rice.

The Power of Inbreeding： NGS-Based GWAS of Rice Reveals Convergent Evolution during Rice Domestication

Low-coverage whole-genome sequencing is an effective strategy for genome-wide association studies in hu- mans, due to the availability of large reference panels for genotype imputation. However, it is unclear whether this strategy can be utilized in other species without reference panels. Using simulations, we show that this approach is even more relevant in inbred species such as rice （Oryza sativa L.）, which are effectively haploid, allowing easy haplotype construction and imputation-based genotype calling, even without the availability of large reference panels. We sequenced 203 rice varieties with well-characterized phenotypes from the United States Department of Agriculture Rice Mini-Core Collection at an average depth of 1.5~ and used the data for mapping three traits. For the first two traits, amylose content and seed length, our approach leads to direct identification of the previously identified causal SN Ps in the major-effect loci. For the third trait, pericarp color, an important trait underwent selection during domestication, we identified a new major-effect locus. Although known loci can explain color variation in the varieties of two main subspecies of Asian domesticated rice,japonica and indica, the new locus identified is unique to another domesticated rice subgroup, aus, and together with existing loci, can fully explain the major variation in pericarp color in aus. Our discovery of a unique genetic basis of white pericarp in aus provides an example of convergent evolution during rice domestication and suggests that aus may have a domestication history independent of japonica and indica.