Core Ideas
Genome‐wide association study (GWAS) for rice quality was performed in two breeding populations.
Twenty‐two putative quantitative trait loci (QTL) were associated to rice quality.
A genomic region on chromosome 6 was associated with all quality traits in the tropical japonica population.
Markers for favorable haplotypes are ready for immediate use for selection.
Rice (Oryza sativa 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 tropical japonica population that was associated with all quality traits and we identified favorable haplotypes. Furthermore, this region is linked to the OsBEI gene that codes for a starch branching enzyme I, which is implicated in starch granule formation. In tropical japonica, we also found two putative QTL linked to OsBEII, OsDEP1, and OsDEP2. 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.
In this work we classify all the order-two Hypergeometric operators D, symmetric with respect to some 2 × 2 irreducible matrix-weight W such that DPn = Pn λn 0 0 µn with no repetition among the eigenvalues {λn, µn} n∈N 0 , where {Pn} n∈N 0 is the (unique) sequence of monic orthogonal polynomials with respect to W .We obtain, in a very explicit way, a three parameter family of such operators and weights. We also give the corresponding monic orthongonal polynomials, their three term recurrence relation and their squared matrix-norms.2010 Mathematics Subject Classification. 42C05; 47S10; 33C45.
Drought stress is one of the most important factors limiting soybean [Glycine max (L.) Merr.] productivity and reducing yield stability. Soybean breeders need phenotypic and genotypic tools to improve drought stress tolerance, but most of available strategies are expensive and unaffordable for small‐scale public breeding programs. In this study, elite germplasm of a locally adapted breeding population was used to estimate a yield stability index as an indicator of drought response. In order to associate yield stability of analyzed genotypes to drought response, water deficit scenarios related to the crop cycle group were defined. Four groups of genotypes were identified in relation to yield stability: two groups showed stables yield (without interaction with water deficit scenarios), and two groups showed unstable yield (with crossover interaction with water deficit scenarios). This phenotypic information was used to identify genomic regions and candidate genes associated with yield stability index. A new method for the definition of a quantitative trait loci (QTL) region was developed based on the probability of marker pairwise of belonging to four linkage disequilibrium (LD) categories. Seven QTL were found and their implication on drought tolerance was further supported by linkage to previously reported QTL for water use efficiency trait.
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