Hesham A. Agrama

Association mapping of stigma and spikelet characteristics in rice (Oryza sativa L.)

Stigma and spikelet characteristics play an essential role in hybrid seed production. A mini-core of 90 accessions developed from USDA rice core collection was phenotyped in field grown for nine traits of stigma and spikelet and genotyped with 109 DNA markers, 108 SSRs plus an indel. Three major clusters were built upon Rogers’ genetic distance, indicative of indicas, and temperate and tropical japonicas. A mixed linear model combining PC-matrix and K-matrix was adapted for mapping marker-trait associations. Resulting associations were adjusted using false discovery rate technique. We identified 34 marker-trait associations involving 22 SSR markers for eight traits. Four markers were associated with single stigma exsertion (SStgE), six with dual exsertion (DStgE) and five with total exsertion. RM5_Chr1 played major role indicative of high regression with not only DStgE but also SStgE. Four markers were associated with spikelet length, three with width and seven with L/W ratio. Numerous markers were co-associated with multiple traits that were phenotypically correlated, i.e. RM12521_Chr2 associated with all three correlated spikelet traits. The co-association should improve breeding efficiency because single marker could be used to assist breeding for multiple traits. Indica entry 1032 (cultivar 50638) and japonica entry 671 (cultivar Linia 84 Icar) with 80.65 and 75.17% of TStgE, respectively are recommended to breeder for improving stigma exsertion.

Allelic Analysis of Sheath Blight Resistance with Association Mapping in Rice

Sheath blight (ShB) caused by the soil-borne pathogen Rhizoctonia solani is one of the most devastating diseases in rice world-wide. Global attention has focused on examining individual mapping populations for quantitative trait loci (QTLs) for ShB resistance, but to date no study has taken advantage of association mapping to examine hundreds of lines for potentially novel QTLs. Our objective was to identify ShB QTLs via association mapping in rice using 217 sub-core entries from the USDA rice core collection, which were phenotyped with a micro-chamber screening method and genotyped with 155 genome-wide markers. Structure analysis divided the mapping panel into five groups, and model comparison revealed that PCA5 with genomic control was the best model for association mapping of ShB. Ten marker loci on seven chromosomes were significantly associated with response to the ShB pathogen. Among multiple alleles in each identified loci, the allele contributing the greatest effect to ShB resistance was named the putative resistant allele. Among 217 entries, entry GSOR 310389 contained the most putative resistant alleles, eight out of ten. The number of putative resistant alleles presented in an entry was highly and significantly correlated with the decrease of ShB rating (r = −0.535) or the increase of ShB resistance. Majority of the resistant entries that contained a large number of the putative resistant alleles belonged to indica, which is consistent with a general observation that most ShB resistant accessions are of indica origin. These findings demonstrate the potential to improve breeding efficiency by using marker-assisted selection to pyramid putative resistant alleles from various loci in a cultivar for enhanced ShB resistance in rice.

Genotypic and phenotypic characterization of genetic differentiation and diversity in the USDA rice mini-core collection

A rice mini-core collection consisting of 217 accessions has been developed to represent the USDA core and whole collections that include 1,794 and 18,709 accessions, respectively. To improve the efficiency of mining valuable genes and broadening the genetic diversity in breeding, genetic structure and diversity were analyzed using both genotypic (128 molecular markers) and phenotypic (14 numerical traits) data. This mini-core had 13.5 alleles per locus, which is the most among the reported germplasm collections of rice. Similarly, polymorphic information content (PIC) value was 0.71 in the mini-core which is the highest with one exception. The high genetic diversity in the mini-core suggests there is a good possibility of mining genes of interest and selecting parents which will improve food production and quality. A model-based clustering analysis resulted in lowland rice including three groups, aus (39 accessions), indica (71) and their admixtures (5), upland rice including temperate japonica (32), tropical japonica (40), aromatic (6) and their admixtures (12) and wild rice (12) including glaberrima and four other species of Oryza. Group differentiation was analyzed using both genotypic distance Fst from 128 molecular markers and phenotypic (Mahalanobis) distance D2 from 14 traits. Both dendrograms built by Fst and D2 reached similar-differentiative relationship among these genetic groups, and the correlation coefficient showed high value 0.85 between Fst matrix and D2 matrix. The information of genetic and phenotypic differentiation could be helpful for the association mapping of genes of interest. Analysis of genotypic and phenotypic diversity based on genetic structure would facilitate parent selection for broadening genetic base of modern rice cultivars via breeding effort.

Unraveling the complex trait of harvest index with association mapping in rice (Oryza sativa L.).

Harvest index is a measure of success in partitioning assimilated photosynthate. An improvement of harvest index means an increase in the economic portion of the plant. Our objective was to identify genetic markers associated with harvest index traits using 203 O. sativa accessions. The phenotyping for 14 traits was conducted in both temperate (Arkansas) and subtropical (Texas) climates and the genotyping used 154 SSRs and an indel marker. Heading, plant height and weight, and panicle length had negative correlations, while seed set and grain weight/panicle had positive correlations with harvest index across both locations. Subsequent genetic diversity and population structure analyses identified five groups in this collection, which corresponded to their geographic origins. Model comparisons revealed that different dimensions of principal components analysis (PCA) affected harvest index traits for mapping accuracy, and kinship did not help. In total, 36 markers in Arkansas and 28 markers in Texas were identified to be significantly associated with harvest index traits. Seven and two markers were consistently associated with two or more harvest index correlated traits in Arkansas and Texas, respectively. Additionally, four markers were constitutively identified at both locations, while 32 and 24 markers were identified specifically in Arkansas and Texas, respectively. Allelic analysis of four constitutive markers demonstrated that allele 253 bp of RM431 had significantly greater effect on decreasing plant height, and 390 bp of RM24011 had the greatest effect on decreasing panicle length across both locations. Many of these identified markers are located either nearby or flanking the regions where the QTLs for harvest index have been reported. Thus, the results from this association mapping study complement and enrich the information from linkage-based QTL studies and will be the basis for improving harvest index directly and indirectly in rice.

Exploring Genetic and Spatial Structure of U.S. Weedy Red Rice (Oryza sativa) in Relation to Rice Relatives Worldwide

Abstract Weedy red rice is a highly troublesome weed of rice in the United States and throughout the world. Effective management of this weed has remained challenging to U.S. farmers, partly because of the biological diversity among red rice populations, resistance to or avoidance of control measures, and genetic similarities with crop rice that allow crossing between the two plant types. The aim of this research was to identify simple sequence repeat (SSR) marker loci that will unambiguously differentiate between U.S. weedy red rice, commercial rice cultivars, and their hybrids, to characterize the genetic diversity and structure of U.S. weedy red rice accessions in relation to Oryza collections from international sources, and to relate genetic and geographic variability within U.S. weedy red rice. Thirty-one SSR markers were used to analyze 180 worldwide Oryza entries and 80 U.S. weedy red rice and U.S. rice cultivars. Twenty-six of the 31 SSR marker loci were highly informative with respect to genetic distinctions between U.S. weedy red rice and U.S. rice cultivars. U.S. red rice are accessions clustered into two main SSR-based collections, awnless strawhull (SA−) and awned blackhull (BA+), according to genetic distance analysis and principal coordinate analysis. Genetic structure analysis clearly identified SA− and BA+ red rice, rice–red rice hybrids, commercial japonica rice cultivars, indica rice, and a number of international and wild Oryza spp. standards (e.g., Oryza nivara, Oryza rufipogon, and Oryza glaberrima) as genetically distinct groups. U.S. SA− red rice exhibited greater spatial structure than did BA+ in that the genetic makeup of SA− accessions changed nearly twice as much with geographic distance as compared to BA+. However, the overall genetic variability within SA− red rice accessions was less than for BA+ accessions, suggesting that the SA− types may be genetically less compatible than BA+ types with other Oryza plants such as rice or other red rice types present in U.S. rice fields. Several of the awned red rice entries exhibited evidence of natural hybridization with different red rice types. Our results suggest that the SA− and BA+ red rice collections have different genetic backgrounds. SA− accessions generally associated most closely with indica-like red- or white-bran Oryza sativa cultivar standards, while BA+ accessions generally associated more closely with O. nivara or O. nivara–like O. sativa entries. Although the U.S. red rice accessions appear not to have descended directly from introductions of the worldwide Oryza standards analyzed, an Oryza red-pericarp entry from Niger (UA 1012; PI 490783) was genetically very similar to some U.S. BA+ accessions. Nomenclature: Oryza nivara Sharma and Shastry; Oryza rufipogon Griff.; red rice, O. sativa L.; O. glaberrima Steud.; rice, O. sativa L. ORSAT.

Genetic diversity associated with conservation of endangered Dongxiang wild rice (Oryza rufipogon)

The wild progenitor species (Oryza rufipogon) of Asian cultivated rice (O. sativa L.) is located in Dongxiang county, China which is considered its the northernmost range worldwide. Nine ex situ and three in situ populations of the Dongxiang wild rice (DXWR) and four groups of modern cultivars were genotyped using 21 SSR markers for study of population structure, conservation efficiency and genetic relationship. We demonstrated that the ex situ conservation of the DXWR failed to maintain the genetic identity and reduced genetic diversity. Therefore, in situ conservation is absolutely necessary to maintain the genetic identity, diversity and heterozygosity. Also, in situ conservation is urgently needed because natural populations in DXWR have decreased from nine to three at present due to farming activity and urban expansion. In DXWR, the three surviving in situ populations had greater expected heterozygosity than any cultivated rice, and were genetically closer to japonica than either the male-sterile maintainer or restorer lines, or indica. Japonica has the lowest genetic diversity of cultivated rice. As a result, DXWR is a rich gene pool and is especially valuable for genetic improvement of japonica rice because these O. rufipogon accessions are most closely related to the japonica as compared to O. rufipogon collected anywhere else in the world.

Combining ability under drought stress relative to SSR diversity in common wheat

Eight-parental diallel cross and SSR molecular markers were used to determine the combining ability of common wheat lines grown under well-watered (WW) and water-stress (WS) conditions. Analysis of variance of yield indicated highly significant differences among the progenies. General combining ability (GCA) determined most of the differences among the crosses. Specific combing ability (SCA) was also significant but less important. The estimates of GCA effects indicated that one line was the best general combiner for grain yield under drought. Nei’s genetic distance, measured using SSR markers, differed from 0.20 to 0.48 among the eight genotypes. The correlation of Nei’s genetic distance with SCA for grain yield and heterosis ranged from 0.4 to 0.5. These results indicate that the level of SCA and heterosis depends on the level of genetic diversity between the wheat genotypes examined. Microsatellite markers were effective in predicting the mean and the variance of SCA in various cultivars combinations. However, selection of crosses solely on microsatellite data would miss superior combinations.

Genetic Analysis of Atypical U.S. Red Rice Phenotypes: Indications of Prior Gene Flow in Rice Fields?

Abstract Weedy red rice is a troublesome weed problem in rice fields of the southern United States. Typically, red rice plants are much taller than rice cultivars, and most biotypes are either awnless with straw-colored hulls (strawhull) or have long awns with black-colored hulls (blackhull). Outcrossing between rice and red rice occurs at low rates, resulting in a broad array of plant types. Simple sequence repeat (SSR) markers were used to evaluate the genetic backgrounds of atypical red rice types obtained from rice farms in Arkansas, Louisiana, Missouri, and Mississippi, in comparison to standard red rice types and rice cultivars. Principal coordinates analysis (PCoA) and population structure analysis of atypical red rice accessions suggested that short-stature awnless (LhtsA−) and awned (LhtsA+) types, each representing a total of about 5% of a 460-accession collection, usually were closely genetically related to their normal-sized counterparts, and not with cultivated rice. A short-awned, intermediate height type, ‘Sawn’, representing about 4% of the accessions was genetically distinct from all of the other types. Key alleles in Sawn types appeared to be shared by both standard awnless (StdRRA−) and awned (StdRRA+) red rice, suggesting that Sawn types could have arisen from gene flow between awned and awnless red rice types. Nomenclature: Weedy red rice, Oryza sativa L.; Rice, Oryza sativa L.

Evaluation of a M-202 × Oryza nivara advanced backcross mapping population for seedling vigor, yield components and quality

AbstractOryza nivara, the ancestral species of cultivated rice (O. sativa), has been the source of novel alleles for resistance to biotic and abiotic stress lost during domestication. Interspecific advanced backcross (ABC) populations permit the introgression of desirable alleles from the wild species into O. sativa and allow traits to be mapped to chromosomal regions by QTL mapping. An ABC population was developed by crossing M-202, a California medium grain, temperate japonica cultivar with O. nivara (IRGC100195). The population has 177 BC2F2:5 progeny lines and was evaluated for 17 traits including seedling vigor under cool temperature (mesocotyl, coleoptile, shoot and root lengths), agronomic (days to heading, plant height, culm angle, panicle type), yield components (panicles per plant, panicle length, florets and seeds per panicle, 100-seed weight) and quality [kernel length and width, apparent amylose content (AAC), alkali spreading value (ASV)]. Most exciting was that the O. nivara parent improved seedling vigor by increasing both the coleoptile and shoot lengths. Wild donor alleles increased the panicles per plant and seed weight, but M-202 alleles improved fertility. For one locus, the O. nivara alleles accounted for increased kernel length even though this parent had smaller seeds than M-202. The AAC mapped to the WAXY locus and ASV to the ALK locus, with most progeny being similar to M-202 for these quality traits. Select progeny lines could be useful for improving seedling vigor. This interspecific population is the first in the background of a U.S. temperate japonica rice cultivar.

Application of Molecular Markers in Breeding for Nitrogen Use Efficiency

Summary Nitrogen use efficiency (NUE) is defined as dry matter yield produced per unit of N supplied and available in the soil. NUE is approximately 33% for cereal production worldwide. Increased cereal NUE must accompany increased yield needed to feed the growing world population. Consequently, continued efforts are needed to include plant selection under low N input which is not often considered a priority by plant breeders. Molecular markers have accelerated plant breeding in a number of areas including biotic (disease and insect) resistance and abiotic (drought, low nitrogen fertilization and frost) tolerance. Marker-based technology has already provided scientists with a powerful approach for identifying and mapping quantitative trait loci (QTL) and would lead to the development of a better understanding of genetic phenomena. Two main NUE studies have been discussed. The first study identified QTL for NUE in maize involved the grain yield and secondary morphological traits of interest, such as plant height, ear leaf area, ears per plant and kernels per ear. This was compared with second study of QTL for yield and its components with genes encoding cytolistic gult-amine synthestase and leaf N03 - content. These secondary traits were correlated with yield and demonstrated segregation with high heritability under low nitrogen conditions. Marker assisted selection (MAS) should be able to offer significant advantages in cases where phenotypic screening is particularly expensive or difficult, including breeding projects involving multiple genes, recessive genes, late expression of the trait of interest, seasonal considerations, or geographical considerations. In addition to reducing costs of conventional breeding, MAS also has the potential to generate time savings. Possibly, the greatest contribution of QTL mapping to plant breeding will be the basic understanding of the genetic architecture of quantitative traits, thereby relating specific genetic loci with the biological mechanisms associated with desirable phenotypes.