Wengui Yan

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.

Water Management Impacts on Arsenic Speciation and Iron-Reducing Bacteria in Contrasting Rice-Rhizosphere Compartments

Rice cultivated on arsenic (As) contaminated-soils will accumulate variable grain-As concentrations, as impacted by varietal differences, soil variables, and crop management. A field-scale experiment was conducted to study the impact of intermittent and continuous flooding on As speciation and microbial populations in rice rhizosphere compartments of soils that were either historically amended with As pesticide or unamended with As. Rhizosphere-soil, root-plaque, pore-water and grain As were quantified and speciated, and microbial populations in rhizosphere soil and root-plaque were characterized. Total-As concentrations in rhizosphere and grain were significantly lower in intermittently flooded compared to the continuously flooded plots (86% lower in pore-water, 55% lower in root-plaque and 41% lower in grain samples). iAs(V), iAs(III), and DMAs(V) were the predominant As species detected in rhizosphere-soil and root-plaque, pore-water and grain samples, respectively. Relative proportions of Archaea and iron-reducing bacteria (FeRB) were higher in rhizosphere soil compared to root-plaque. In rhizosphere soil, the relative abundance of FeRB was lower in intermittently flooded compared to continuously flooded plots, but there were no differences between root-plaque samples. This study has demonstrated that reductions in dissolved As concentrations in the rhizosphere and subsequent decreases in grain-As concentration can be attained through water management.

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.

Red Rice (Oryza sativa) Plant Types Affect Growth, Coloration, and Flowering Characteristics of First- and Second-Generation Crosses with Rice1

Red rice is a major weed of rice in the southern U.S. and can intercross with rice. Knowledge of the plant phenotypes from such crosses would be valuable for identification and management of these plants. Male-sterile long-grain tropical japonicas ‘Kaybonnet-1789’ and ‘Cypress-1819’ were crossed with two awned and two awnless U.S. red rice types. F1 plants produced pubescent leaves, red pericarp, and medium-grain seeds. Crosses involving awned LA3 and TX4 red rice produced F1 plants with reddish-purple basal leaf sheaths and usually flowered within the same time periods as the parents, whereas those involving awnless StgS red rice had green basal leaf sheaths, flowered much later than either parent, and produced awnless F1 and F2 offspring. Crosses involving awned red rice produced F1 plants with long awns and F2 plants with awns ranging in length from zero to that of red rice parents. F1 plants were taller than either parent and produced intermediate culm angles similar to red rice, whereas F2 plants had culms ranging from erect (like rice) to more open than red rice. Thus, true F1 hybrids from crosses between pure breeding (homozygous) rice and red rice can be positively identified by a combination of traits including pubescent leaves, medium-grain seeds with red pericarps, open plant types, and heights greater than the red rice parent. F1 hybrids may be awned or awnless, have purple or green stems, or have normal or delayed heading. F2 plants have a broad combination of phenotypic traits found in both parents and F1 hybrids. Nomenclature: Red rice, Oryza sativa L. #3 ORYSA, ‘LA3’, ‘Stuttgart strawhull’, ‘TX4’; rice, Oryza sativa L., ‘KBNT-1789’, ‘CPRS-1819’. Additional index words: Ecotype, biotype, gene flow, gene segregation, hybrid, outcrossing, phenotypic traits, rice, red rice, weedy rice. Abbreviations: IMI, imidazolinone; MS, male sterile; PCR, polymerase chain reaction; QTL, quantitative trait loci.

Weed Suppression Potential of ‘Rondo’ and Other Indica Rice Germplasm Lines

Abstract Research was conducted to evaluate the weed suppression potential of ‘Rondo’ (4484-1693; PI 657830), a sister line (4484-1665), and other indica rice lines against barnyardgrass in field plots in Stuttgart, AR, using minimal herbicide inputs in two separate 3-yr experiments. Under weed pressure, Rondo and the sister line (4484-1665) generally produced yields that were comparable to those of weed-suppressive indica standards and approximately 50% greater than those of the least-suppressive commercial cultivars, such as ‘Kaybonnet’, ‘Katy’, and ‘Lemont’. Rice yield under weed pressure was correlated with weed-free yield and harvest height. Indica lines tended to produce more tillers than did the commercial cultivars. Tillering potential under weed-free conditions was not correlated with weed suppression or yield loss; however, tillering under weed pressure was strongly correlated with weed suppression and biomass, and yield and yield loss under the weed densities in these experiments. Rondo is presently being used for commercial organic rice production in Texas, in part due to its high yield potential and ability to suppress or tolerate rice pests, including weeds. Our results suggest that the weed-suppressive ability of Rondo and the other indica lines evaluated in these experiments is superior to that of many commercial cultivars. Nomenclature: Barnyardgrass, Echinochloa crus-galli (L.) Beauv.; rice, Oryza sativa L.

Development of genetic markers linked to straighthead resistance through fine mapping in rice (Oryza sativa L.).

Straighthead, a physiological disorder characterized by sterile florets and distorted spikelets, causes significant yield losses in rice, and occurs in many countries. The current control method of draining paddies early in the season stresses plants, is costly, and wastes water. Development of resistant cultivar is regarded as the most efficient way for its control. We mapped a QTL for straighthead resistance using two recombinant inbred line (RIL) F9 populations that were phenotyped over two years using monosodium methanearsonate (MSMA) to induce the symptoms. One population of 170 RILs was genotyped with 136 SSRs and the other population of 91 RILs was genotyped with 159 SSRs. A major QTL qSH-8 was identified in an overlapping region in both populations, and explained 46% of total variation in one and 67% in another population for straighthead resistance. qSH-8 was fine mapped from 1.0 Mbp to 340 kb using 7 SSR markers and further mapped to 290 kb in a population between RM22573 and InDel 27 using 4 InDel markers. SSR AP3858-1 and InDel 11 were within the fine mapped region, and co-segregated with straighthead resistance in both RIL populations, as well as in a collection of diverse global accessions. These results demonstrate that AP3858-1 and InDel 11 can be used for marker-assisted selection (MAS) for straighthead resistant cultivars, which is especially important because there is no effective way to directly evaluate straighthead resistance.

Erratum to: Genetic analysis of genetic basis of a physiological disorder “straighthead” in rice (Oryza sativa L.)

Unfortunately, the original version of this article contains a few errors. Figure 2 in the original publication, qSTH-2 and qSTH-8 is quite displaced, and the arrow for qSTH-8 is not shown. The corrected figure is shown in this erratum. Moreover, the third author, Hesham Agrama, has added another affiliation. His additional affiliation is: Department of Crop Sciences, College of Agricultural and Marine Sciences Sultan Qaboos University P.O. Box 34, Alkhoud 123, Oman.