Integrating Molecular Markers and Environmental Covariates To Interpret Genotype by Environment Interaction in Rice (Oryza sativa L.) Grown in Subtropical Areas.

Understanding the genetic and environmental basis of genotype × environment interaction (G×E) is of fundamental importance in plant breeding. If we consider G×E in the context of genotype × year interactions (G×Y), predicting which lines will have stable and superior performance across years is an important challenge for breeders. A better understanding of the factors that contribute to the overall grain yield and quality of rice (Oryza sativa L.) will lay the foundation for developing new breeding and selection strategies for combining high quality, with high yield. In this study, we used molecular marker data and environmental covariates (EC) simultaneously to predict rice yield, milling quality traits and plant height in untested environments (years), using both reaction norm models and partial least squares (PLS), in two rice breeding populations (indica and tropical japonica). We also sought to explain G×E by differential quantitative trait loci (QTL) expression in relation to EC. Our results showed that PLS models trained with both molecular markers and EC gave better prediction accuracies than reaction norm models when predicting future years. We also detected milling quality QTL that showed a differential expression conditional on humidity and solar radiation, providing insight for the main environmental factors affecting milling quality in subtropical and temperate rice growing areas.

Genome-Wide Association Study Using Historical Breeding Populations Discovers Genomic Regions Involved in High-Quality Rice.

Rice ( L.) is one of the most important staple food crops in the world; however, there has recently been a shift in consumer demand for higher grain quality. Therefore, understanding the genetic architecture of grain quality has become a key objective of rice breeding programs. Genome-wide association studies (GWAS) using large diversity panels have successfully identified genomic regions associated with complex traits in diverse crop species. Our main objective was to identify genomic regions associated with grain quality and to identify and characterize favorable haplotypes for selection. We used two locally adapted rice breeding populations and historical phenotypic data for three rice quality traits: yield after milling, percentage of head rice recovery, and percentage of chalky grain. We detected 22 putative quantitative trait loci (QTL) in the same genomic regions as starch synthesis, starch metabolism, and cell wall synthesis-related genes are found. Additionally, we found a genomic region on chromosome 6 in the population that was associated with all quality traits and we identified favorable haplotypes. Furthermore, this region is linked to the gene that codes for a starch branching enzyme I, which is implicated in starch granule formation. In , we also found two putative QTL linked to , , and . Our study provides an insight into the genetic basis of rice grain chalkiness, yield after milling, and head rice, identifying favorable haplotypes and molecular markers for selection in breeding programs.

Resistance to Multiple Temperate and Tropical Stem and Sheath Diseases of Rice.

Stem rot and aggregated sheath spot are the two major stem and sheath diseases affecting rice (Oryza sativa L.) in temperate areas. A third fungal disease, sheath blight, is a major disease in tropical areas. Resistance to these diseases is a key objective in rice breeding programs but phenotyping is challenged by the confounding effects of phenological and morphological traits such as flowering time (FT) and plant height (PH). This study sought to identify quantitative trait loci (QTL) for resistance to these three diseases after removing the confounding effects of FT and PH. Two populations of advanced breeding germplasm, one with 316 tropical japonica and the other with 325 indica genotypes, were evaluated in field and greenhouse trials for resistance to the diseases. Phenotypic means for field and greenhouse disease resistance, adjusted by FT and PH, were analyzed for associations with 29,000 single nucleotide polymorphisms (SNPs) in tropical japonica and 50,000 SNPs in indica. A total of 29 QTL were found for resistance that were not associated with FT or PH. Multilocus models with selected resistance-associated SNPs were fitted for each disease to estimate their effects on the other diseases. A QTL on chromosome 9 accounted for more than 15% of the phenotypic variance for the three diseases. When resistance-associated SNPs at this locus from both the tropical japonica and indica populations were incorporated into the model, resistance was improved for all three diseases with little impact on FT and PH.

One-step, codominant detection of imidazolinone resistance mutations in weedy rice (Oryza sativa L. )

Background Weedy rice (Oryza sativa L.) is a noxious form of cultivated rice (O. sativa L.) associated with intensive rice production and dry seeding. A cost-efficient strategy to control this weed is the Clearfield rice production system, which combines imidazolinone herbicides with mutant imidazolinone-resistant rice varieties. However, imidazolinone resistance mutations can be introgressed in weedy rice populations by natural outcrossing, reducing the life span of the Clearfield technology. Timely and accurate detection of imidazolinone resistance mutations in weedy rice may contribute to avoiding the multiplication and dispersion of resistant weeds and to protect the Clearfield system. Thus, highly sensitive and specific methods with high throughput and low cost are needed. KBioscience's Allele Specific PCR (KASP) is a codominant, competitive allele-specific PCR-based genotyping method. KASP enables both alleles to be detected in a single reaction in a closed-tube format. The aim of this work is to assess the suitability and validity of the KASP method for detection in weedy rice of the three imidazolinone resistance mutations reported to date in rice. Results Validation was carried out by determining the analytical performance of the new method and comparing it with conventional allele-specific PCR, when genotyping sets of cultivated and weedy rice samples. The conventional technique had a specificity of 0.97 and a sensibility of 0.95, whereas for the KASP method, both parameters were 1.00. Conclusions The new method has equal accuracy while being more informative and saving time and resources compared with conventional methods, which make it suitable for monitoring imidazolinone-resistant weedy rice in Clearfield rice fields.