Identification for quantitative trait loci controlling grain shattering in rice

Seed shattering is an important factor causing loss of grain yield before and during rice harvest. In the present study, the quantitative trait loci regarding shattering scale, breaking tensile strength (BTS) and abscission layer (AL), the parameters evaluating seed shattering habit by hand gripping, a digital force gauge and observation on AL, respectively, were identified by using an doubled haploid line (DHL) population from a cross between a loose-shattering type Tongil variety, ‘Samgang’, and a moderately difficult shattering japonica variety, ‘Nagdong’. Eight QTLs consisted in four QTLs for shattering scale, two QTLs for AL, each one QTL for pulling and bending strength were detected on six chromosomes, respectively. Among them, Qss1 with flanking markers RM6696 and RM476 explained 31% of phenotype variation in shattering scale. Furthermore, two new QTLs controlling shattering habit, Qss5-2 and Qal5-1, were located on chromosome 5 at the interval 5028–5037 and 5021-RM289. They explained 10% and 12% of phenotype variations, respectively. A total of eleven digenic epistatic loci were identified for four parameters. The identification of QTLs affecting seed shattering habits is favorable to thoroughly dissect the genetic mechanism of the shattering habit and to apply for marker-assisted selection in rice breeding system of specific regions.     

Identification of main effects, epistatic effects and their environmental interactions of QTLs for yield traits in rice

Quantitative trait loci (QTLs) controlling yield and yield components were identified by using a doubled haploid (DH) population of 120 lines from a sub-specific cross between ‘Samgang’ (Indica) and ‘Nagdong’ (Japonica). Main effects, epistatic effects, their environment interactions of QTLs were analyzed via mixed linear model approach across different environments. A total of 17 putative QTLs were identified on 8 chromosomes and five QTLs were detected over two years. 7 QTLs of main effects and 23 epistatic interactions were observed for five traits. Epistatic interactions played an important role in controlling the expression of yield related traits. The epistatic effects explained higher percentages of phenotype variation for panicles per plant, seed set percentage and yield. Significant QTL×environment (QE) interactions effects were identified for all traits, including 5 main effect QTLs. However, the present study failed to identify the significant interactions between epistatic loci containing main effect QTLs and the environment. The information provided in the present study could be used in the marker-assisted selection to enhance selection efficiency and to improve yield in rice.     

QTL mapping of black rot (Guignardia bidwellii) resistance in the grapevine rootstock ‘Börner’ (V. riparia Gm183 × V. cinerea Arnold)

Key message

In the grapevine cultivar ‘Börner’ QTLs for black rot resistance were detected consistently in several independent experiments. For one QTL on chromosome 14 closely linked markers were developed and a detailed map provided.

Abstract

Black rot is a serious grapevine disease that causes substantial yield loss under unfavourable conditions. All traditional European grapevine cultivars are susceptible to the causative fungus Guignardia bidwellii which is native to North America. The cultivar ‘Börner’, an interspecific hybrid of V. riparia and V. cinerea, shows a high resistance to black rot. Therefore, a mapping population derived from the cross of the susceptible breeding line V3125 (‘Schiava grossa’ × ‘Riesling’) with ‘Börner’ was used to carry out QTL analysis. A resistance test was established based on potted plants which were artificially inoculated in a climate chamber with in vitro produced G. bidwellii spores. Several rating systems were developed and tested. Finally, a five class scheme was applied for scoring the level of resistance. A major QTL was detected based on a previously constructed genetic map and data from six independent resistance tests in the climate chamber and one rating of natural infections in the field. The QTL is located on linkage group 14 (Rgb1) and explained up to 21.8 % of the phenotypic variation (LOD 10.5). A second stable QTL mapped on linkage group 16 (Rgb2; LOD 4.2) and explained 8.5 % of the phenotypic variation. These two QTLs together with several minor QTLs observed on the integrated map indicate a polygenic nature of the black rot resistance in ‘Börner’. A detailed genetic map is presented for the locus Rgb1 with tightly linked markers valuable for the development for marker-assisted selection for black rot resistance in grapevine breeding.     

Quantitative trait loci associated with androgenic responsiveness in triticale (×Triticosecale Wittm.) anther culture

Quantitative trait loci (QTLs) associated with androgenic responsiveness in triticale were analyzed using a population of 90 DH lines derived from the F1 cross between inbred line ‘Saka 3006’ and cv. ‘Modus’, which was used in a number of earlier studies on molecular mapping in this crop. Using Windows QTL Cartographer and MapQTL 5.0, composite interval mapping (CIM) and association studies (Kruskal–Wallis test; K–W) for five androgenesis parameters (androgenic embryo induction, total regeneration and green plant regeneration ability, and two characteristics describing final androgenesis efficiency) were conducted. For the studied components of androgenic response, CIM detected in total 28 QTLs which were localized on 5 chromosomes from A and R genomes. Effects of all QTLs that were identified at 2.0 or above of the LOD score explained 5.1–21.7?% of the phenotypic variation. Androgenesis induction was associated with seven QTLs (LOD between 2.0 and 5.8) detected on chromosomes 5A, 4R, 5R and 7R, all of them confirmed by K–W test as regions containing the markers significantly linked to the studied trait. What is more, K–W test revealed additional markers on chromosomes: 5A, 2BL, 7B and 5R. Both total and green regeneration ability were controlled by genes localized on chromosome 4A. Some of the QTLs that affected final androgenesis efficiency were identical with those associated with androgenic embryo induction efficiency, suggesting that the observed correlation may be either due to tight linkage or to pleiotropy. Key message Five regions of the triticale genome were indicated as revealing significant marker/trait association. Markers located in these regions are potentially useful for triticale breeding through marker-assisted selection.     

Genetic dissection of root growth in rice (Oryza sativa L.). II: mapping quantitative trait loci using molecular markers

Drought is a major abiotic stress of upland rice, and good root growth has been associated with drought avoidance. We report on the genetic mapping of root growth traits in an F₂ population derived from two drought-resistant rice varieties, ‘Bala’ and ‘Azucena’. Restriction fragment length polymorphism (RFLP) between the parents was 32%, and a molecular map with 71 marker loci and 17 linkage groups covering 1280 cM was produced. Quantitative trait loci (QTLs) for eight root growth characteristics were mapped using phenotype data obtained in a hydroponic screen previously described in a companion paper. Using a significance threshold of LOD 2.4, we observed one QTL for maximum root length after 28 days growth on chromosome 11. It had a LOD score of 6.9, explained nearly 30% of the variation and appeared to be largely additive in effect. QTLs for maximum root length after 3, 7, 14 and 21 days of growth were also revealed. Some root-length QTLs, including that on chromosome 11, varied greatly with developmental stage. One QTL for root volume and two QTLs for adventitious root thickness were detected. No QTLs were detected for the length of cells in the mature (fully expanded) zone of adventitious root tips. The results obtained are discussed in the context of previous reports on mapping root growth parameters in rice.     

High-resolution mapping of two rice brown planthopper resistance genes, Bph20(t) and Bph21(t), originating from Oryza minuta

Brown planthopper (BPH) is one of the most destructive insect pests of rice. Wild species of rice are a valuable source of resistance genes for developing resistant cultivars. A molecular marker-based genetic analysis of BPH resistance was conducted using an F₂ population derived from a cross between an introgression line, ‘IR71033-121-15’, from Oryza minuta (Accession number 101141) and a susceptible Korean japonica variety, ‘Junambyeo’. Resistance to BPH (biotype 1) was evaluated using 190 F₃ families. Two major quantitative trait loci (QTLs) and two significant digenic epistatic interactions between marker intervals were identified for BPH resistance. One QTL was mapped to 193.4-kb region located on the short arm of chromosome 4, and the other QTL was mapped to a 194.0-kb region on the long arm of chromosome 12. The two QTLs additively increased the resistance to BPH. Markers co-segregating with the two resistance QTLs were developed at each locus. Comparing the physical map positions of the two QTLs with previously reported BPH resistance genes, we conclude that these major QTLs are new BPH resistance loci and have designated them as Bph20(t) on chromosome 4 and Bph21(t) on chromosome 12. This is the first report of BPH resistance genes from the wild species O. minuta. These two new genes and markers reported here will be useful to rice breeding programs interested in new sources of BPH resistance.     

Identification of a novel gene, H34, in wheat using recombinant inbred lines and single nucleotide polymorphism markers

Hessian fly (HF), Mayetiola destructor, is an important pest of wheat (Triticum aestivum L.) worldwide. Because it has multiple biotypes that are virulent to different wheat HF resistance genes, pyramiding multiple resistance genes in a cultivar can improve resistance durability, and finding DNA markers tightly linked to these genes is essential to this process. This study identified quantitative trait loci (QTLs) for Hessian fly resistance (HFR) in the wheat cultivar ‘Clark’ and tightly linked DNA markers for the QTLs. A linkage map was constructed with single nucleotide polymorphism and simple sequence repeat markers using a population of recombinant inbred lines (RILs) derived from the cross ‘Ning7840’ × ‘Clark’ by single-seed descent. Two QTLs associated with resistance to fly biotype GP were identified on chromosomes 6B and 1A, with the resistance alleles contributed from ‘Clark’. The QTL on 6B flanked by loci Xsnp921 and Xsnp2745 explained about 37.2 % of the phenotypic variation, and the QTL on 1A was flanked by Xgwm33 and Xsnp5150 and accounted for 13.3 % of phenotypic variation for HFR. The QTL on 6B has not been reported before and represents a novel wheat gene with resistance to HF, thus, it is designated H34. A significant positive epistasis was detected between the two QTLs that accounted for about 9.5 % of the mean phenotypic variation and increased HFR by 0.16. Our results indicated that different QTLs may contribute different degrees of resistance in a cultivar and that epistasis may play an important role in HFR.     

Molecular Genetic Analysis of QTLs for Ferulic Acid Content in Dried Straw of Rice (Oryza sativa L.)

Phenolic acids are secondary metabolic organic compounds produced by plants and often are mentioned as allelochemicals. This study was conducted to determine the genetic basis controlling the ferulic acid content of rice straw in a recombinant inbred (RI) population derived from a cross between a japonica variety, Asominori, with a higher content of ferulic acid, and an indica variety, IR24, with a lower content, using 289 RFLP markers. Continuous distributions and transgressive segregations of ferulic acid content were observed in the RI population, which showed that ferulic acid content in rice straw was quantitatively inherited. Single marker analysis and composite interval mapping identified three quantitative trait loci (QTLs) for ferulic acid content with LOD values of 2.03 (chromosome 3), 3.16 (chromosome 6), and 3.06 (chromosome 7); all three had increased additive effects (13.5, 18.3, and 18.1 g g ^–1) from the Asominori parent and accounted for 5.5, 16.9, and 12.8% of total phenotypic variation, respectively. This is the first report on the identification of QTLs associated with ferulic acid and their chromosomal localization on the molecular map of rice. The tightly linked molecular markers that flank the QTLs might be useful in breeding and selection of varieties with higher phenolic acid content.     

Genetic dissection of rice blast resistance by QTL mapping approach using an F3 population

Rice blast is one of the major fungal diseases that badly reduce rice production in Asia including Malaysia. There is not much information on identification of QTLs as well as linked markers and their association with blast resistance within local rice cultivars. In order to understanding of the genetic control of blast in the F₃ families from indica rice cross Pongsu seribu2/Mahsuri, an analysis of quantitative trait loci against one of the highly virulent Malaysian rice blast isolate Magnaporthe oryzae, P5.0 was carried out. Result indicated that partial resistance to this pathotype observed in the present study was controlled by multiple loci or different QTLs. In QTL analysis in F₃ progeny fifteen QTLs on chromosomes 1, 2, 3, 5, 6, 11 and 12 for resistance to blast nursery tests was identified. Three of detected QTLs (qRBr-6.1, qRBr-11.4, and qRBr-12.1) had significant threshold (LOD >3) and approved by both IM and CIM methods. Twelve suggestive QTLs, qRBr-1.2, qRBr-2.1, qRBr-4.1, qRBr-5.1, qRBr-6.2, qRBr-6.3, qRBr-8.1, qRBr-10.1, qRBr-10.2, qRBr-11.1, qRBr-11.2 and qRBr-11.3) with Logarithmic of Odds (LOD) <3.0 or LRS <15) were distributed on chromosomes 1, 2, 4, 5, 6, 8, 10, and 11. Most of the QTLs detected using single isolate had the resistant alleles from Pongsu seribu 2 which involved in the resistance in the greenhouse. We found that QTLs detected for deferent traits for the using isolate were frequently located in similar genomic regions. Inheritance study showed among F₃ lines resistance segregated in the expected ratio of 15: 1 for resistant to susceptible. The average score for blast resistance measured in the green house was 3.15, 1.98 and 29.95 % for three traits, BLD, BLT and % DLA, respectively.     

Genetic analysis of sugar-related traits in rice grain

Sugar is the primary product of photosynthesis in plant and plays a critical role in regulating plant growth and development. In this study, quantitative trait loci (QTLs) for total soluble sugar, sucrose, and fructose contents in rice grain were identified using a double haploid population derived from a cross between japonica CJ06 and indica TN1. A total of 17 QTLs, including four QTLs for total soluble sugar content, seven QTLs for sucrose content, and six QTLs for fructose content, were detected on chromosome 1, 3, 4, 5, 6, and 8, with the LOD ranges from 2.61 to 3.85. Furthermore, among the determined varieties, we found that the total soluble sugar content in japonica showed higher than that in indica. Comparative genetic analysis showed that starch synthesis related gene is presumably involved in sugar-related metabolic activity in rice grain.     

Quantitative trait locus (QTL) analysis of fruit-quality traits for mandarin breeding in Japan

The improvement of fruit quality is an important objective in citrus breeding. Using an F₁ segregating population from a cross between citrus cultivars ‘Harehime’ (‘E647’—‘Kiyomi’ [Citrus unshiu Marcow. ‘Miyagawa Wase’ × Citrus sinensis (L.) Osbeck ‘Trovita’] × ‘Osceola’—a cultivar of clementine [Citrus clementina hort. ex Tanaka] × ‘Orland’ [Citrus paradisi Macfad. ‘Duncan’ × Citrus tangerina hort. ex Tanaka] × ‘Miyagawa Wase’) and ‘Yoshida’ ponkan (Citrus reticulata Blanco ‘Yoshida’), a SNP-based genetic linkage map was constructed and quantitative trait locus (QTL) mapping of four fruit-quality traits (fruit weight, sugar content, peel puffing, and water rot) was performed. The constructed genetic linkage map of ‘Harehime’ consisted of 442 single nucleotide polymorphisms (SNPs) on 9 linkage groups (LGs) and covered 635.8 cM of the genome, while that of ‘Yoshida’ ponkan consisted of 332 SNPs on 9 LGs and covered 892.9 cM of its genome. We identified four QTLs associated with fruit weight, one QTL associated with sugar content, three QTLs associated with peel puffing, and one QTL associated with water rot. For these QTL regions, we estimated the haplotypes of the crossed parents and verified the founding cultivars that these QTLs were originated from and their inheritance in descendant cultivars using pedigree information. QTLs identified in this study provide useful information for marker-assisted breeding of citrus in Japan.     

Identification and Validation of Quantitative Trait Loci for Agronomic Traits in Advanced Backcross Breeding Lines Derived from Oryza rufipogon × Oryza sativa Cultivar MR219

A backcross breeding strategy was used to identify quantitative trait loci (QTLs) associated with 14 traits in a BC₂F₂ population derived from a cross between MR219, an indica rice cultivar and an accession of Oryza rufipogon (IRGC 105491). A total of 261 lines were genotyped with 96 microsatellite markers and evaluated for plant morphology, yield components and growth period. The genetic linkage map generated for this population with an average interval size of 16.2?cM, spanning 1,553.4?cM (Kosambi) of the rice genome. Thirty-eight QTLs were identified with composite interval mapping (CIM), whereas simple interval mapping (SIM) resulted in 47 QTLs (LOD >3.0). The O. rufipogon allele was favourable for 59% of QTLs detected through CIM. Of 261 BC₂F₂ families, 26 advanced backcross breeding lines (BC₂F₅) were used for QTL validation. These lines were selected on the basis of the yield traits potentiality in BC₂F₃ and BC₂F₄ generations. The field trial was conducted at three different locations in Malaysia using randomized complete block design with three replications. Trait based marker analysis was done for QTL determination. Twenty-five QTLs were detected in BC₂F₅ generation whereas 29 QTLs were detected in BC₂F₂ generation of the same population. Two QTLs (qPL-1 and qSPL-7) were not considered for validation due to their low R ² values and two QTLs (qPSS-3-2 and qGW-3-2) were not detected in the BC₂F₅ population. Fifteen QTLs showed the beneficial effect to enhance the trait value of the breeding lines. QTL validation aided to select the promising lines for further utilization.     

Phenotyping at hot spots and tagging of QTLs conferring spot blotch resistance in bread wheat

Spot blotch is a major foliar disease of wheat caused by Bipolaris sorokiniana in warm and humid environments of the world including South Asian countries. In India, it has a larger impact in Indo-Gangetic plains of the country. Therefore, the present study was undertaken to phenotype a mapping population at different hot spots of India and to detect quantitative trait loci (QTL) for resistance to spot blotch in wheat. For this study, 209 single seed descent (SSD) derived F₈, F₉, F₁₀ recombinant inbred lines (RILs) of the cross ‘Sonalika’ (an Indian susceptible cultivar)/‘BH 1146’ (a Brazilian resistant cultivar) were assessed for spot blotch resistance at two hot spot locations (Coochbehar and Kalyani) for three years and for two years under controlled conditions in the polyhouse (Karnal). The population showed large variation in spot blotch reaction for disease severity in all the environments indicating polygenic nature of the disease. Microsatellite markers were used to create the linkage maps. Joint and/or individual year analysis by composite interval mapping (CIM) and likelihood of odds ratio (LOD) >2.1, detected two consistent QTLs mapped on chromosome 7BL and 7DL and these explained phenotypic variation of 11.4 percent and 9.5 percent over the years and locations, respectively. The resistance at these loci was contributed by the parent ‘BH 1146’ and shown to be independent of plant height and earliness. Besides, association of some agro-morphological traits has also been observed with percent disease severity. These identified genomic regions may be used in future wheat breeding programs through marker assisted selection for developing spot blotch resistant cultivars.     

Identification of QTL for agronomic traits of importance for olive breeding

Development of methodologies for early selection is one of the most important goals of olive breeding programs at present. In this context, the identification of molecular markers associated with beneficial alleles could allow the development of marker-assisted selection (MAS) strategies in olive breeding programs. Fruit-related and plant vigor traits, which are of key importance for olive selection and breeding, were analyzed during two seasons in a progeny derived from the cross ‘Picual’ × ‘Arbequina.’ Quantitative trait loci (QTL) analyses were performed using MapQTL 4.0. A total of 22 putative QTLs were identified in the map of ‘Arbequina.’ QTLs clustered in linkage groups (LG) 1, 10 and 17. QTLs for oil-related traits located in LG 1 and 10 explained around 20–30 % of the phenotypic variability depending on the season and the trait. QTL for moisture-related traits were detected in LG 1, 10 and 17, and QTLs for the ratio pulp to stone were identified in LG 10 and 17 explaining around 15–20 %. Interaction between QTLs for the same trait was investigated. The significance of these results was discussed considering the co-localization of QTLs and Pearson correlations among traits. Five additional QTLs were detected in the map of ‘Picual.’ Four of them clustered in LG 17 indicating the presence of a QTL for fruit weight explaining around 12.7–15.2 % of the variability. Additionally, a QTL for trunk diameter was detected in LG 14 explaining 16 % of the variation. These results represent an important step toward the application of MAS in olive breeding programs.     

Quantitative Trait Locus Mapping and Candidate Gene Analysis for Plant Architecture Traits Using Whole Genome Re-Sequencing in Rice

Plant breeders have focused on improving plant architecture as an effective means to increase crop yield. Here, we identify the main-effect quantitative trait loci (QTLs) for plant shape-related traits in rice (Oryza sativa) and find candidate genes by applying whole genome re-sequencing of two parental cultivars using next-generation sequencing. To identify QTLs influencing plant shape, we analyzed six traits: plant height, tiller number, panicle diameter, panicle length, flag leaf length, and flag leaf width. We performed QTL analysis with 178 F₇ recombinant in-bred lines (RILs) from a cross of japonica rice line ‘SNUSG1’ and indica rice line ‘Milyang23’. Using 131 molecular markers, including 28 insertion/deletion markers, we identified 11 main- and 16 minor-effect QTLs for the six traits with a threshold LOD value > 2.8. Our sequence analysis identified fifty-four candidate genes for the main-effect QTLs. By further comparison of coding sequences and meta-expression profiles between japonica and indica rice varieties, we finally chose 15 strong candidate genes for the 11 main-effect QTLs. Our study shows that the whole-genome sequence data substantially enhanced the efficiency of polymorphic marker development for QTL fine-mapping and the identification of possible candidate genes. This yields useful genetic resources for breeding high-yielding rice cultivars with improved plant architecture.     

Genetic Analysis and QTL Detection for Resistance to White Tip Disease in Rice

The inheritance of resistance to white tip disease (WTDR) in rice (Oryza sativa L.) was analyzed with an artificial inoculation test in a segregating population derived from the cross between Tetep, a highly resistant variety that was identified in a previous study, and a susceptible cultivar. Three resistance-associated traits, including the number of Aphelenchoides besseyi (A. besseyi) individuals in 100 grains (NA), the loss rate of panicle weight (LRPW) and the loss rate of the total grains per panicle (LRGPP) were analyzed for the detection of the quantitative trait locus (QTL) in the population after construction of a genetic map. Six QTLs distributed on chromosomes 3, 5 and 9 were mapped. qNA3 and qNA9, conferring reproduction number of A. besseyi in the panicle, accounted for 16.91% and 12.54% of the total phenotypic variance, respectively. qDRPW5a and qDRPW5b, associated with yield loss, were located at two adjacent marker intervals on chromosome 5 and explained 14.15% and 14.59% of the total phenotypic variation and possessed LOD values of 3.40 and 3.39, respectively. qDRPW9 was considered as a minor QTL and only explained 1.02% of the phenotypic variation. qLRGPP5 contributed to the loss in the number of grains and explained 10.91% of the phenotypic variation. This study provides useful information for the breeding of resistant cultivars against white tip disease in rice.     

水稻籼粳交DH群体收获指数及源库性状的QTL分析

以 1个水稻籼粳交 (圭 6 30 0 2 4 2 8)来源的DH群体为材料 ,利用 1张含有 2 32个标记的RFLP连锁图谱和基于混合线性模型的定位软件QTLMapper1 0对水稻收获指数及生物量、籽粒产量、库容量和株高 5个性状进行QTL分析 ,共检测到 2 1个主效应QTLs和 9对上位性互作位点。其中 ,控制籽粒产量的 3个QTLs合计贡献率为 4 2 % ,LOD值为 7 10 ;这 3个QTLs或者与收获指数的QTL同位 ,或者与生物量的QTL同位 ,且加性效应的方向一致 ,从而揭示了“籽粒产量 =生物量×收获指数”的遗传基础所在。控制收获指数的 4个QTLs合计贡献率为 4 6 % ,LOD值为 10 3;控制生物量的 4个QTLs合计贡献率为 6 4 % ,LOD值为 14 0 9;收获指数的 4个QTLs与生物量的 4个QTLs均不同位。因此 ,通过基因重组 ,可能实现控制收获指数和生物量的增效基因的聚合 ,由此获得收获指数和生物量“双高”的基因型。检测到 5个株高QTLs,其合计贡献率为 6 4 % ,LOD值为 11 6 2 ;其中 ,有 3个效应较小的QTLs与生物量、库容量和 或籽粒产量QTLs同位 ,且同位QTLs的加性效应方向一致 ;未发现株高QTLs与收获指数QTLs的同位性。由此表明 ,株高与“源 流 库”概念中的“源”和“库”在遗传上有一定程度的关联 ,而与“流”无关联。此外还发现 ,在上述同位性QTL     

Mapping Genetic Loci for Quantitative Traits of Golden Shell Color,Mineral Element Contents,and Growth-Related Traits in Pacific Oyster (<Emphasis Type="Italic">Crassostrea gigas</Emphasis>)

Golden shell color and mineral content are important economic traits of Pacific oyster (Crassostrea gigas). In this study, we mapped a series of quantitative trait loci (QTLs) that control zinc (Zn) and magnesium (Mg) content, shell color and growth performance to two sex-averaged linkage maps from the FAM-A and FAM-B families. In total, ten QTLs were identified in seven linkage groups (LGs) in the FAM-B family, and seven QTLs were identified in four linkage groups in the FAM-A family. Two QTLs affecting the trait of golden shell color were identified in LG8 of the FAM-A and LG10 of the FAM-B families, which could explain 20.2 and 10.5% of the phenotypic variations, respectively. Two QTLs for Zn content were identified that could contribute to 17.9 and 34.44% of the phenotypic variations in FAM-A. Six QTLs for Zn and Mg contents were identified in four LGs (LG1, LG2, LG5, and LG9) in FAM-B, which explained 13.5–26.7% of the phenotypic variations. In addition, seven QTLs related to oyster growth were recognized in both FAM-A and FAM-B families accounting for 14.6–36.7% of the phenotypic variations. All of the DNA markers in QTL regions were blasted and 14 genes associated with above traits were identified. The mRNA expression of these genes was determined by quantitative RT-PCR. These QTLs and candidate genes could be used as potential targets for marker-assisted selection in C. gigas breeding.     

Identification of quantitative trait loci for grain size and the contributions of major grain-size QTLs to grain weight in rice

Grain weight, one of the three major components of rice yield, is largely determined by grain size, which is controlled by quantitative trait loci (QTLs). In a previous study, we identified qGS5 as a major QTL for grain width. Here, we report our identification of two more major grain-size QTLs (qGL3 and qGW2a) by using a recombinant inbred line (RIL) population from a cross of two indica varieties, ‘Zhenshan 97’ and ‘SLG’. To investigate the contribution of the three grain-size QTLs to final grain weight, we developed near-isogenic lines (NILs) NIL-qGL3, NIL-qGW2a, and NIL-qGS5 and used these to build the combined QTLs–NIL in the genetic background of ‘Zhenshan 97’ by marker-assisted selection and conventional backcrossing, respectively. A BCF₂ population of 957 individuals was developed from the combined QTLs-NIL for further study of the genetic control of grain size. The QTL analysis revealed that qGW2a and qGL3 played more important roles in grain weight gain than qGS5. All three QTLs showed additive effects with respect to grain weight, with no interaction. These results clearly indicate that pyramiding of major grain-size QTLs is a useful approach for improving rice yield.     

QTLs for hybrid fertility and their association with female and male sterility in rice

Hybrid sterility is one of the major barriers to the application of wide crosses in plant breeding and is commonly encountered in crosses between indica and japonica rice varieties. Ten mapping populations comprised of two reciprocal F2 and eight BC₁F₁ populations generated from the cross between Ilpumbyeo (japonica) and Dasanbyeo (indica) were used to identify QTLs and to interpret the gametophytic factors involved in hybrid fertility or sterility between two subspecies. Frame maps were constructed using a total of 107 and 144 STS markers covering 12 rice chromosomes in two reciprocal F2 and eight BC₁F₁ populations, respectively. A total of 15 main-effect QTLs and 17 significant digenic-epistatic interactions controlling spikelet fertility (SF) were resolved in the entire genome map of F₂ and BC₁F₁ populations. Among detected QTLs responsible for hybrid fertility, four QTLs, qSF5.1 and qSF5.2 on chromosome 5, qSF6.2 on chromosome 6, and qSF12.2 on chromosome 12, were identified as major QTLs since they were located at corresponding positions in at least three mapping populations. Loci qSF5.1, qSF6.1 and qSF6.2 were responsible for both female and male sterility, whereas qSF3.1, qSF7 and qSF12.2 affected the spikelet fertility only through embryosac factors, and qSF9.1 did through pollen factors. Five new QTLs identified in this study will be helpful for understanding the hybrid sterility and for breeding programs via inter-subspecific hybridization.