Anna M. McClung

Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa

Asian rice, Oryza sativa is a cultivated, inbreeding species that feeds over half of the worlds population. Understanding the genetic basis of diverse physiological, developmental, and morphological traits provides the basis for improving yield, quality and sustainability of rice. Here we show the results of a genome-wide association study based on genotyping 44,100 SNP variants across 413 diverse accessions of O. sativa collected from 82 countries that were systematically phenotyped for 34 traits. Using cross-population-based mapping strategies, we identified dozens of common variants influencing numerous complex traits. Significant heterogeneity was observed in the genetic architecture associated with subpopulation structure and response to environment. This work establishes an open-source translational research platform for genome-wide association studies in rice that directly links molecular variation in genes and metabolic pathways with the germplasm resources needed to accelerate varietal development and crop improvement.

Microsatellites and a single-nucleotide polymorphism differentiate apparentamylose classes in an extended pedigree of US rice germ plasm

Abstract The Waxy gene (Wx) encodes the granule-bound starch synthase responsible for the synthesis of amylose in rice (Oryza sativa). Recently, a polymorphic microsatellite sequence closely linked to the Wx gene was reported. To determine whether polymorphism in this sequence correlates with variation in apparent amylose content, we tested an extended pedigree of 92 current and historically important long-, medium- and short-grain US rice cultivars representing the efforts of many breeders over more than 80 years. Seven Wx microsatellite alleles were identified which together explained 82.9% of the variation in apparent amylose content of the 89 non-glutinous rice cultivars tested. Similar results were also obtained with 101 progenyof a cross between low- and intermediate-amylose breeding lines. An additional, unique microsatelliteallele, (CT)16, was detected in one glutinous cultivar,CI 5309. However, the other glutinous cultivars,Calmochi 101 and Tatsumi mochi, were in the (CT)17 class along with three other cultivars that contained15–16.5% amylose.We sequenced a 200-bp PCR-amplified fragment containing the CT microsatellite and the putative 5′ splice site of the Wx leader intron from a subset of 42 cultivars representing all eight microsatellite alleles. All of the cultivars with 18% or less amylose had the sequence AGTTATA at the putative leader intron 5′ splice site, while all cultivars with a higher proportionof amylose had AGTTATA. This single nucleotidesubstitution could also be assayed by AccI digestion of the amplified fragment. Overall, this single nucleotide polymorphism could explain 79.7% of the variation in the apparent amylose content of the 89 non-glutinous cultivars tested. Interestingly, cultivars in the (CT)19 microsatellite classes that differed substantially in amylose content still showed the correlation between this G-T polymorphism and apparent amylose content. The G-T polymorphism at this site was not, however, able to explain the very low amylose contents of the three glutinous cultivars tested, all of which had the sequence AGTTATA.

Selection under Domestication: Evidence for a Sweep in the Rice Waxy Genomic Region

Rice (Oryza sativa) was cultivated by Asian Neolithic farmers >11,000 years ago, and different cultures have selected for divergent starch qualities in the rice grain during and after the domestication process. An intron 1 splice donor site mutation of the Waxy gene is responsible for the absence of amylose in glutinous rice varieties. This mutation appears to have also played an important role in the origin of low amylose, nonglutinous temperate japonica rice varieties, which form a primary component of Northeast Asian cuisines. Waxy DNA sequence analyses indicate that the splice donor mutation is prevalent in temperate japonica rice varieties, but rare or absent in tropical japonica, indica, aus, and aromatic varieties. Sequence analysis across a 500-kb genomic region centered on Waxy reveals patterns consistent with a selective sweep in the temperate japonicas associated with the mutation. The size of the selective sweep (>250 kb) indicates very strong selection in this region, with an inferred selection coefficient that is higher than similar estimates from maize domestication genes or wild species. These findings demonstrate that selection pressures associated with crop domestication regimes can exceed by one to two orders of magnitude those observed for genes under even strong selection in natural systems.

Genomic Diversity and Introgression in O. sativa Reveal the Impact of Domestication and Breeding on the Rice Genome

Background The domestication of Asian rice (Oryza sativa) was a complex process punctuated by episodes of introgressive hybridization among and between subpopulations. Deep genetic divergence between the two main varietal groups (Indica and Japonica) suggests domestication from at least two distinct wild populations. However, genetic uniformity surrounding key domestication genes across divergent subpopulations suggests cultural exchange of genetic material among ancient farmers. Methodology/Principal Findings In this study, we utilize a novel 1,536 SNP panel genotyped across 395 diverse accessions of O. sativa to study genome-wide patterns of polymorphism, to characterize population structure, and to infer the introgression history of domesticated Asian rice. Our population structure analyses support the existence of five major subpopulations (indica, aus, tropical japonica, temperate japonica and GroupV) consistent with previous analyses. Our introgression analysis shows that most accessions exhibit some degree of admixture, with many individuals within a population sharing the same introgressed segment due to artificial selection. Admixture mapping and association analysis of amylose content and grain length illustrate the potential for dissecting the genetic basis of complex traits in domesticated plant populations. Conclusions/Significance Genes in these regions control a myriad of traits including plant stature, blast resistance, and amylose content. These analyses highlight the power of population genomics in agricultural systems to identify functionally important regions of the genome and to decipher the role of human-directed breeding in refashioning the genomes of a domesticated species.

Correlation Between Cooked Rice Texture and Rapid Visco Analyser Measurements

ABSTRACT Although amylose content is considered the most important determinant of cooked rice texture, this constituent falls short as a predictor, because cultivars with similar amylose contents may differ in textural properties. Thus, amylography is used as one of a battery of tests, in addition to measuring amylose content, to improve differentiation of cultivars. The purpose of our study was to determine how well amylography conducted with a Rapid Visco Analyser (RVA) serves as a predictor of cooked rice texture, alone and in combination, with amylose content. Textural properties of 87 samples representing short-, medium-, and long-grain rice cultivars were assessed by descriptive sensory and instrumental texture profile (TPA) analyses and related to RVA measurements. None of the cooked rice textural attributes, whether measured by descriptive analysis or TPA, were modeled by RVA with high accuracy (i.e., high r2). Sensory texture attributes cohesiveness of mass, stickiness, and initial starchy coatin...

Through the genetic bottleneck: O. rufipogon as a source of trait-enhancing alleles for O. sativa

This paper summarizes results from a decade of collaborative research using advanced backcross (AB) populations to a) identify quantitative trait loci (QTL) associated with improved performance in rice and to b) clone genes underlying key QTLs of interest. We demonstrate that AB-QTL analysis is capable of (1) successfully uncovering positive alleles in wild germplasm that were not obvious based on the phenotype of the parent (2) offering an estimation of the breeding value of exotic germplasm, (3) generating near isogenic lines that can be used as the basis for gene isolation and also as parents for further crossing in a variety development program and (4) providing gene-based markers for targeted introgression of alleles using marker-assisted-selection (MAS). Knowledge gained from studies examining the population structure and evolutionary history of rice is helping to illuminate a long-term strategy for exploiting and simultaneously preserving the well-partitioned gene pools in rice.

Prediction of cooked rice texture quality using near-infrared reflectance analysis of whole-grain milled samples

ABSTRACT Rice quality is based on chemical and physical properties affecting its appearance, flavor, and texture characteristics. Sensory quality can be assessed by a combination of descriptive sensory and physicochemical property evaluations. The purpose of the present study was to assess the potential of near-infrared reflectance spectroscopy (NIRS) and NIRS in combination with other physicochemical measurements for the determination of sensory texture attributes in whole-grain milled rice samples. Six rice samples representing combinations of variety and growing locations received treatments of two degrees of milling and five drying conditions to achieve final moisture levels of 12 or 15% (n = 120). Quality measurements of the cooked rice included sensory and instrumental texture analyses. Quality measurements of the uncooked rice included amylose and protein (chemical reference), whiteness, transparency, and degree of milling (appearance units of milled rice), and NIRS analyses. Partial least squares ...

Effects of Postharvest Processing on Texture Profile Analysis of Cooked Rice

ABSTRACT The effects of drying conditions, final moisture content, and degree of milling on the texture of cooked rice varieties, as measured by texture profile analysis, were investigated. Instrumentally measured textural properties were not significantly (α = 0.05) affected by drying conditions, with the exception of cohesiveness. Cohesiveness was lower in rice dried at lower temperatures (18°C or ambient) than in that dried at the higher commercial temperatures. Final moisture content and degree of milling significantly (α = 0.05) affected textural property values for adhesiveness, cohesiveness, hardness, and springiness; their effects were interdependent. The effects of deep milling were more pronounced in the rice dried to 15% moisture than that dried to 12%. In general, textural property values for hardness were higher and those for cohesiveness, adhesiveness, and springiness were lower in regular-milled rice dried to 15% moisture than in that dried to 12%. In contrast, hardness values were lower an...

Rapid Determination of Rice Cultivar Responses to the Sheath Blight Pathogen Rhizoctonia solani Using a Micro-Chamber Screening Method

An accurate greenhouse screening method has not been developed previously to identify host response to sheath blight disease caused by Rhizoctonia solani Kühn that causes significant economic losses in rice yield worldwide. The unavailability of a robust screening system in the greenhouse has made it difficult to quantify disease reactions to R. solani, and has hampered studies on the genetics of resistance and plant breeding efforts to improve resistance. In an effort to develop a standardized laboratory micro-chamber screening method to quantify resistance to R. solani in rice, five rice cultivars, representing a wide range of observed disease reactions under field conditions, were examined in a blind inoculation test at three locations (Arkansas, Texas, and Colombia). Rice seedlings were inoculated at the three- to four-leaf stage with potato dextrose agar plugs containing mycelium and then covered with a 2- or 3-liter transparent plastic bottle for maintaining high humidity after inoculation. Two cultivars, Jasmine 85 and Lemont, that consistently have shown the highest and lowest levels of resistance, respectively, in previous field and greenhouse studies, were used as standards. Concurrent field experiments in Arkansas and Texas also were performed to compare the greenhouse disease ratings with those observed under field conditions. Overall, the relative disease ratings of the seven test cultivars were consistent between test locations and with field evaluations. Thus, the micro-chamber screening method can be used as an effective approach to accurately quantify resistance to the sheath blight pathogen under controlled greenhouse conditions and should help expedite the selection process to improve resistance to this important pathogen.

Effects of Degree of Milling, Drying Condition, and Final Moisture Content on Sensory Texture of Cooked Rice

ABSTRACT Different cultures have different preferences for cooked rice flavor and texture characteristics. These differences provide opportunities for U.S. rice varieties to fit into global markets to meet consumer demands worldwide. It is important to assess the properties of U.S. rice varieties and determine the factors that influence their eating quality. Cooked rice texture attributes can be affected by postharvest handling practices, such as degree of milling, drying condition, and final moisture. This article reports the effects of postharvest handling parameters on the texture of cooked medium- and short-grain rice varieties grown in Arkansas (AR) and California (CA), as measured by descriptive sensory analysis. The rice samples were Bengal (AR), Koshihikari (AR), Koshihikari (CA), M-401 (AR), M-401 (CA), and M-202 (CA). The six rice varieties were regular- or deepmilled and dried under one of five drying conditions to achieve final moisture levels of 12 or 15% (n = 120). A trained sensory panel de...