James W. Stansel

Convergent domestication of cereal crops by independent mutations at corresponding genetic Loci.

Independent domestication of sorghum, rice, and maize involved convergent selection for large seeds, reduced disarticulation of the mature inflorescence, and daylength-insensitive flowering. These similar phenotypes are largely determined by a small number of quantitative trait loci (QTLs) that correspond closely in the three taxa. The correspondence of these QTLs transcends 65 million years of reproductive isolation. This finding supports models of quantitative inheritance that invoke relatively few genes, obviates difficulties in map-based cloning of QTLs, and impels the comparative mapping of complex pheno-types across large evolutionary distances, such as those that separate humans from rodents and domesticated mammals.

Identification of quantitative trait loci (QTLs) for heading date and plant height in cultivated rice (Oryza sativa L.)

Abstract‘Lemont’ and ‘Teqing’ are both semidwarf rice varieties that differ in heading date by only 6 days. However, when ‘Lemont’ and ‘Teqing’ are crossed there is transgressive segregation for both heading date (HD) and plant height (PH). By testing 2418 F4 lines with 113 well-distributed RFLP markers, we identified and mapped chromosomal regions that were largely responsible for this transgressive segregation. QHd3a, a QTL from ‘Lemont’ that gives 8 days earlier heading, was identified on chromosome 3 approximately 3 cM from the marker RG348. Another QTL with a large effect, QHd8a, which gives 7 days earlier heading, was identified on chromosome 8 of ‘Teqing’ between RG20 and RG1034. Along with a QTL, QHd9a with a phenotypic effect of 3.5 days, these genomic regions collectively explain 76.5% of the observed phenotypic variance in heading date. Four QTLs which altered plant height from 4 to 7 cm were also mapped; these collectively explain 48.8% of the observed phenotypic variation in plant height. None of the QTLs for plant height mapped to chromosome 1, the location of the semidwarf gene sd-1. All three of the HD loci mapped to approximately the same genomic locations as PH QTLs, and in all cases, there was a reduction in height of approximately 1 cm for every day of earlier heading. The correspondence between the HD and some of the PH loci suggests that genes at these chromosome locations may have pleiotropic effects on both HD and PH. The observed heterosis in the F1 plants for HD can be largely explained by the dominance for earliness of the identified HD loci and distribution of earlier heading alleles in the parents. However, overdominance observed at one of the PH QTL may, at least in part, be responsible for the observed heterosis in PH.

Characterization of quantitative trait loci (QTLs) in cultivated rice contributing to field resistance to sheath blight (Rhizoctonia solani).

Sheath blight, caused by Rhizoctonia solani, is one of the most important diseases of rice. Despite extensive searches of the rice germ plasm, the major gene(s) which give complete resistance to the fungus have not been identified. However, there is much variation in quantitatively inherited resistance to R. solani, and this type of resistance can offer adequate protection against the pathogen under field conditions. Using 255 F4 bulked populations from a cross between the susceptible variety ‘Lemont’ and the resistant variety ‘Teqing’, 2 years of field disease evaluation and 113 well-distributed RFLP markers, we identified six quantitative trait loci (QTLs) contributing to resistance to R. solani. These QTLs are located on 6 of the 12 rice chromosomes and collectively explain approximately 60% of the genotypic variation or 47% of the phenotypic variation in the ‘Lemont’x‘Teqing’ cross. One of these resistance QTLs (QSbr4a), which accounted for 6% of the genotypic variation in resistance to R. solani, appeared to be independent of associated morphological traits. The remaining five putative resistance loci (QSbr2a, QSbr3a, QSbr8a, QSbr9a and QSbr12a) all mapped to chromosomal regions also associated with increased plant height, three of which were also associated with QTLs causing later heading. This was consistent with the observation that heading date and plant height accounted for 47% of the genotypic variation in resistance to R. solani in this population. There were also weak associations between resistance to R. solani and leaf width, which were likely due to linkage with a QTL for this trait rather than to a physiological relationship.

A “defeated” rice resistance gene acts as a QTL against a virulent strain of Xanthomonas oryzae pv. oryzae

Abstract The genetic components responsible for qualitative and quantitative resistance of rice plants to three strains (CR4, CXO8, and CR6) of Xanthomonas oryzae pv. oryzae (Xoo) were investigated using a set of 315 recombinant inbred lines (RILs) from the cross Lemont (japonica) × Teqing (indica) and a complete linkage map with 182 well distributed RFLP markers. We mapped a major gene (Xa4) and ten quantitative trait loci (QTLs) which were largely responsible for segregation of the resistance phenotype in the RILs. The Teqing allele at the Xa4 locus, Xa4T, acted as a dominant resistance gene against CR4 and CXO8. The breakdown of Xa4T-associated resistance mediated by the mutant allele at the avrXa4 locus in the virulent strain CR6 results from significant changes in both gene action (lose of dominance) and the magnitude of gene effect (≈50% reduction). Nevertheless, Xa4T still acted as a recessive QTL with a significant residual effect against CR6. The mutant alleles at the avrXa4 locus in CXO8 and CR6 that lead to a reduction in effect, or “breakdown”, of Xa4T were apparently accompanied by corresponding penalties for their fitness. The quantitative component of resistance to Xoo in the RILs was largely due to a number of resistance QTLs. Most resistance QTLs mapped to genomic locations where major resistance genes and/or QTLs for resistance to Xoo, blast and sheath blight were identified in the same cross. Most QTLs showed consistent levels of resistance against all three Xoo strains. Our results suggest that a high level of durable resistance to Xoo may be achieved by the cumulative effects of multiple QTLs, including the residual effects of “defeated” major resistance genes.

Mapping of four major rice blast resistance genes from 'Lemont' and 'Teqing' and evaluation of their combinatorial effect for field resistance

Abstract A framework linkage map was developed using 284 F10 recombinant inbred lines (RILs) from a ’Lemont’×’Teqing’ rice cultivar cross. Evaluation of a subset of 245 of these RILs with five races of the rice blast pathogen permitted RFLP mapping of three major resistance genes from Teqing and one major gene from Lemont. All mapped genes were found to confer resistance to at least two blast races, but none conferred resistance to all five races evaluated. RFLP mapping showed that the three resistance genes from Teqing, designated Pi-tq5, Pi-tq1 and Pi-tq6, were present on chromosomes 2, 6 and 12, respectively. The resistance gene from Lemont, Pi-lm2, was located on chromosome 11. Pi-tq1 is considered a new gene, based on its reaction to these five races and its unique map location, while the other three genes may be allelic with previously reported genes. Lines with different gene combinations were evaluated for disease reaction in field plots. Some gene combinations showed both direct effects and non-linear interaction. The fact that some of the lines without any of the four tagged genes exhibited useful levels of resistance in the field plots suggests the presence of additional genes or QTLs affecting the blast reaction segregating in this population.

Genetic dissection of the source-sink relationship affecting fecundity and yield in rice (shape Oryza sativa L.)

The genetic basis underlying the relationship between the source leaves (the top two leaves) and the sink capacity in rice was investigated in a replicated trial of 2418 F2 derived F4 progeny from an inter-subspecific cross between cv. Lemont (japonica) and cv. Teqing (indica) and a complete linkage map with 115 well distributed RFLP markers. Path analysis indicated that 50% of the phenotypic variation in the primary sink capacity-grain weight per panicle was attributable to variation of the flag leaf area. Thirteen QTL and 30 pairs of epistatic loci were identified, which influence the length, width and area of the source leaves and the size of the primary sink (panicles) panicle length, floret density and floret number per panicle. Two QTL (QLl3b and QLw4) and 7 pairs of epistatic loci are largely responsible for the observed relationship between the source leaves and the sink capacity. The others appear to primarily influence the shape of the source leaves or panicle length/branching, and contribute little to the observed source-sink relationship and partially explain the yield component compensation. Our results suggest that important QTL affecting the source leaves can be manipulated through marker-assisted selection to increase sink capacity, which might result in improved yield potential in rice.

Mapping QTLs for field resistance to the rice blast pathogen and evaluating their individual and combined utility in improved varieties

Abstract.Lines from a Lemont × Teqing recombinant inbred population were evaluated for dilatory resistance to rice blast disease using: (1) the Standard Evaluation System (SES) for rating leaf blast, (2) the percentage diseased leaf area (%DLA), and (3) the area under a disease progress curve (AUDPC). RFLP mapping using 175 well-distributed loci revealed nine QTLs, one each on chromosomes 1, 2, 3, 4, 6, 7 and 9, with two loci on chromosome 12. All nine putative QTLs were associated with AUDPC, six with both a %DLA and a SES rating. Teqing contributed the resistance allele for all these loci except for the one located on chromosome 4. Individual QTLs accounted for 5–32% of the observed phenotypic variation, and combined QTL models accounted for 43–53%. Three QTLs were located near three of the four major resistance genes previously identified in this population. The resistances of both Lemont and Teqing were attributable to a combination of both major genes capable of inducing hypersensitive reactions and minor genes causing less-distinctive phenotypic differences. Interactions were noted between QTLs and major genes. Our findings are in support of the strategy of pyramiding major genes and QTLs in carefully selected combinations to develop improved varieties with resistance to the blast fungus that is both broad in spectrum and durable.

RFLP facilitated analysis of tiller and leaf angles in rice (Oryza sativa L.)

Plant type is an important composite trait associated with the yield potential in rice and other cereal crops. Several characters associated with the plant type of modern rice cultivars including tiller angle, leaf and flag leaf angle, were investigated using a complete linkage map with 115 well distributed RFLP markers and progeny testing of 2418 F2 derived F4 lines from a cross between O. sativa ssp. japonica cv. ‘Lemont’ and spp. indica cv. ‘Teqing’. One major gene (Ta) and 11 QTLs were largely responsible for the tremendous variation of the three plant type characters in the Lemont/Teqing F2 population. The major gene, Ta, located between RZ228 and RG667 on chromosome 9, accounted for 47.5% of the phenotypic variation in tiller angle and had large pleiotropic effects on both leaf and flag leaf angles. This gene plus four QTLs accounted for 69.1% of the genotypic variation in tiller angle. Eight additional QTLs for leaf and flag leaf angles were also identified, which collectively explained 52.0 and 66.4% of the genotypic variation of these traits. Ta and three QTLs ( QFla2, QFla5 and QFla7) apparently affected the related plant type characters differently, suggesting their possible differential expression in different developmental stages of rice plants or possibly clustering of different genes affecting these traits. Plant type, and consequently grain yield of rice, may be improved by deliberately manipulating these QTLs in a marker-assisted selection program.

RFLP mapping and race specificity of bacterial blight resistance genes (QTLs) in rice.

By using a set of 315 recombinant inbred lines (RILs) from the cross Lemont (japonica) × Teqing (indica) and a complete linkage map with 186 well distributed RFLP markers and 3 morphological markers, a major gene (Xa4) and 10 QTLs and 9 pairs of epistkis loci conferring horizontal resistance to three strains ofXanthomonas orym pvoryza (Xoo) were mapped. The Teqing allele at Xa4 on chromosome 11 acts as a dominant resistant gene against pathogen race CR4 and CX08, but as an additive QTL with a significantly (47%) reduced effect against the virulent strain, CR6. The major gene Xa4 exhibited stronger degree of race specificity. Most QTLs showed consistent levels of resistance against all threeXoo strains. The results suggest that a high level durable resistance toXoo may be achieved by cumulative effects of multiple QTL.

Griffing and Hayman Diallel Analyses of Variance for Eating and Processing Quality Parameters of Milled Rice

Amylose content and amylographic viscosity measurements, both chemical and physical properties of milled rice, arc important eating and processing quality parameters and are characteristics of a endosperm. A six-parent diallel cross was made and, thus, a genetic study on such endosperm characteristics was conducted. Since amylose contern and amylographic viscosity measurements are difficult to be determined on a single grain basis, samples of bulking heterozygous F2 grains from combining homogeneous heterozygous F1 plants were used as measurement units. Results of Griffings and Haymans diallel analyses of variance for the parameters, amylose content and amylographic peak, hot-paste, cool-paste breakdown, setback and consistency viscosities, are respectively presented. It was evident that gene action in the parents studied was mainly additive for all evaluated endosperm characteristics, although dominance effects were also involved. The fact that reciprocal differences in both Griffings and Haymans diallel analyses were not significant indicated that Haymans assumption (2) no differences between reciprocal crosses was met in this study. Date indicated that significant dominance gene effects wer due to a directional dominance effect, an asymmetry of the gene distribution, and a residual dominance effect for all studied quality parameters except for hot-paste viscosity, in which the effect of an asymmetry of the gene distribution was not significant.