A QTL for rice grain yield in aerobic environments with large effects in three genetic backgrounds.

A large-effect QTL associated with grain yield in aerobic environments was identified in three genetic backgrounds, Apo/(2)*Swarna, Apo/(2)*IR72, and Vandana/(2)*IR72, using bulk-segregant analysis (BSA). Apo and Vandana are drought-tolerant aerobic-adapted varieties, while Swarna and IR72 are important lowland rice varieties grown on millions of hectares in Asia but perform poorly in aerobic conditions. Two closely linked rice microsatellite (RM) markers, RM510 and RM19367, located on chromosome 6, were found to be associated with yield under aerobic soil conditions in all three backgrounds. The QTL linked to this marker, qDTY6.1 (DTY, grain yield under drought), was mapped to a 2.2 cM region between RM19367 and RM3805 at a peak LOD score of 32 in the Apo/(2)*Swarna population. The effect of qDTY6.1 was tested in a total of 20 hydrological environments over a period of five seasons and in five populations in the three genetic backgrounds. In the Apo/(2)*Swarna population, qDTY6.1 had a large effect on grain yield under favorable aerobic (R (2) ≤ 66%) and irrigated lowland (R (2) < 39%) conditions but not under drought stress; Apo contributed the favorable allele in all the conditions where an effect was observed. In the Apo/IR72 cross, Apo contributed the favorable allele in almost all the aerobic environments in RIL and BC(1)-derived populations. In the Vandana/IR72 RIL and BC(1)-derived populations, qDTY6.1 had a strong effect on yield in aerobic drought stress, aerobic non-stress, and irrigated lowland conditions; the Vandana allele was favorable in aerobic environments and the IR72 allele was favorable in irrigated lowland environments. We conclude that qDTY6.1 is a large-effect QTL for rice grain yield under aerobic environments and could potentially be used in molecular breeding of rice for aerobic environments.

Identification and characterization of large-effect quantitative trait loci for grain yield under lowland drought stress in rice using bulk-segregant analysis.

An F(4:5) population of 490 recombinant inbred lines (RILs) from the cross Apo/(2*)Swarna was used to detect quantitative trait loci (QTL) with large effects on grain yield under drought stress using bulk-segregant analysis (BSA). Swarna is an important rainfed lowland rice variety grown on millions of hectares in Asia, but is highly susceptible to drought and aerobic soil conditions. Apo is an aerobic-adapted variety with moderate tolerance to drought. Two rice microsatellite (RM) markers, RM324, and RM416, located on chromosomes 2 and 3, respectively, were shown via BSA to be strongly associated with yield under lowland drought stress. The effects of these QTL were tested in a total of eight hydrological environments over a period of 3 years. The QTL linked to RM416 (DTY(3.1)) had a large effect on grain yield under severe lowland drought stress, explaining about 31% of genetic variance for the trait (P < 0.0001). It also explained considerable variance for yield under mild stress in lowland conditions and aerobic environments. To our knowledge this is the first reported QTL that has a large effect on yield in both lowland drought and aerobic environments. The QTL linked to RM324 (DTY(2.1)) had a highly significant effect on grain yield in lowland drought stress (R(2) = 13-16%) and in two aerobic trials. The effect of these QTL on grain yield was verified to be not mainly due to phenology differences. Effects of DTY(3.1) on yield under stress have been observed in several other rice mapping populations studied at IRRI. Results of this study indicate that BSA is an effective method of identifying QTL alleles with large effects on rice yield under severe drought stress. The Apo alleles for these large-effect QTL for grain yield under drought and aerobic conditions may be immediately exploited in marker-assisted-breeding to improve the drought tolerance of Swarna.

QTL detection with bidirectional and unidirectional selective genotyping: marker-based and trait-based analyses.

Selective genotyping of one or both phenotypic extremes of a population can be used to detect linkage between markers and quantitative trait loci (QTL) in situations in which full-population genotyping is too costly or not feasible, or where the objective is to rapidly screen large numbers of potential donors for useful alleles with large effects. Data may be subjected to 'trait-based' analysis, in which marker allele frequencies are compared between classes of progeny defined based on trait values, or to 'marker-based' analysis, in which trait means are compared between progeny classes defined based on marker genotypes. Here, bidirectional and unidirectional selective genotyping were simulated, using population sizes and selection intensities relevant to cereal breeding. Control of Type I error was usually adequate with marker-based analysis of variance or trait-based testing using the normal approximation of the binomial distribution. Bidirectional selective genotyping was more powerful than unidirectional. Trait-based analysis and marker-based analysis of variance were about equally powerful. With genotyping of the best 30 out of 500 lines (6%), a QTL explaining 15% of the phenotypic variance could be detected with a power of 0.8 when tests were conducted at a marker 10 cM from the QTL. With bidirectional selective genotyping, QTL with smaller effects and (or) QTL farther from the nearest marker could be detected. Similar QTL detection approaches were applied to data from a population of 436 recombinant inbred rice lines segregating for a large-effect QTL affecting grain yield under drought stress. That QTL was reliably detected by genotyping as few as 20 selected lines (4.5%). In experimental populations, selective genotyping can reduce costs of QTL detection, allowing larger numbers of potential donors to be screened for useful alleles with effects across different backgrounds. In plant breeding programs, selective genotyping can make it possible to detect QTL using even a limited number of progeny that have been retained after selection.

Cytoplasmic male-sterile synthetics: a new approach to the exploitation of heterosis in rape.

In addition to their application in the production of F1 hybrids in rape (Brassica napus L.), cytoplasmic male-sterility (CMS) systems may be used to produce synthetic varieties with much higher levels of heterozygosity than those expected in conventional rape synthetics. CMS synthetics are produced by compositing a CMS A-line with several male-fertile (MF) B-lines lacking nuclear alleles for fertility restoration, and increasing the resulting mixture by natural pollination. Over generations of increase, pollination of the CMS component by the MF component of the synthetic results in the progressive loss of A-line nuclear genes from the population. The initial proportions of CMS and MF plants are expected to be preserved over several generations of natural pollination if CMS and MF plants are equal in yield. Methods for estimating the heterozygosity level of CMS synthetics, taking into account the proportion of CMS plants, number of MF parents in Syn 0, and selfing rate (s) of MF plants, are presented. If completely inbred Syn 0 parents and s of 0 and 0.75 for CMS and MF plants respectively, are assumed, the heterozygosity level (1-F) of a synthetic derived from four inbred MF parents each comprising 6.25% of Syn 0 and one inbred CMS parent comprising 75% of Syn 0 is predicted to be 0.66 in Syn 5, compared to 0.30 in synthetics derived from four MF parents only. CMS synthetics offer a novel, low-cost approach to the exploitation of heterosis in rape and other species with mixed mating systems in which self-pollination predominates.