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.     

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.     

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.     

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.