Locating QTLs controlling overwintering seedling rate in perennial glutinous rice 89-1 (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.)

A new cold tolerant germplasm resource named glutinous rice 89-1 (Gr89-1, Oryza sativa L.) can overwinter using axillary buds, with these buds being ratooned the following year. The overwintering seedling rate (OSR) is an important factor for evaluating cold tolerance. Many quantitative trait loci (QTLs) controlling cold tolerance at different growth stages in rice have been identified, with some of these QTLs being successfully cloned. However, no QTLs conferring to the OSR trait have been located in the perennial O. sativa L. To identify QTLs associated with OSR and to evaluate cold tolerance. 286 F₁₂ recombinant inbred lines (RILs) derived from a cross between the cold tolerant variety Gr89-1 and cold sensitive variety Shuhui527 (SH527) were used. A total of 198 polymorphic simple sequence repeat (SSR) markers that were distributed uniformly on 12 chromosomes were used to construct the linkage map. The gene ontology (GO) annotation of the major QTL was performed through the rice genome annotation project system. Three main-effect QTLs (qOSR2, qOSR3, and qOSR8) were detected and mapped on chromosomes 2, 3, and 8, respectively. These QTLs were located in the interval of RM14208 (35,160,202 base pairs (bp))–RM208 (35,520,147 bp), RM218 (8,375,236 bp)–RM232 (9,755,778 bp), and RM5891 (24,626,930 bp)–RM23608 (25,355,519 bp), and explained 19.6%, 9.3%, and 11.8% of the phenotypic variations, respectively. The qOSR2 QTL displayed the largest effect, with a logarithm of odds score (LOD) of 5.5. A total of 47 candidate genes on the qOSR2 locus were associated with 219 GO terms. Among these candidate genes, 11 were related to cell membrane, 7 were associated with cold stress, and 3 were involved in response to stress and biotic stimulus. OsPIP1;3 was the only one candidate gene related to stress, biotic stimulus, cold stress, and encoding a cell membrane protein. After QTL mapping, a total of three main-effect QTLs—qOSR2, qOSR3, and qOSR8—were detected on chromosomes 2, 3, and 8, respectively. Among these, qOSR2 explained the highest phenotypic variance. All the QTLs elite traits come from the cold resistance parent Gr89-1. OsPIP1;3 might be a candidate gene of qOSR2.     

Identification of quantitative trait loci for resistance to rice black-streaked dwarf virus disease and small brown planthopper in rice

Small brown planthopper (SBPH) and its transmitted rice black-streaked dwarf virus disease (RBSDVD) cause serious damage to rice (Oryza sativa L.) production. Though breeding of resistant cultivars is believed to be one of the most important strategies for RBSDVD management, few high-resistance lines have been found to date. In the present study, we identified an indica variety, 9194, that is highly resistant to RBSDVD and analyzed the quantitative trait loci (QTLs) underlying this resistance . In total, four QTLs for RBSDVD resistance, viz. qRBSDV3, qRBSDV6, qRBSDV9, and qRBSDV11, were identified. Among them, qRBSDV6, qRBSDV9, and qRBSDV11 with LOD (logarithm [base 10] of odds) scores of 4.42–4.48, 2.11–7.26, and 5.01–7.16 were repeatedly detected in 2 years, accounting for 10.3–16.7%, 8.3–35.5%, and 20.0–31.1% of the total phenotypic variation, respectively. Further, introgression of single- or multiple-resistance QTLs into a susceptible rice variety by marker-assisted selection (MAS) indicated that stacking the QTLs could progressively enhance RBSDVD resistance, suggesting that these QTLs act additively. The same population was also used for QTL mapping of SBPH resistance. Four QTLs, viz. qSBPH1, qSBPH5, qSBPH8, and qSBPH9, with LOD scores of 2.72, 2.78, 2.15, and 2.85 were detected, explaining 13.7%, 11.0%, 12.0%, and 21.0% of the phenotypic variation, respectively. The identification of RBSDVD and SBPH resistance QTLs, and the development of single and multiple genes with pyramided lines, in this study provides innovative resources for molecular breeding of resistant rice cultivars.     

Improvement of seedling and panicle blast resistance in <Emphasis Type="Italic">Xian</Emphasis> rice varieties following <Emphasis Type="Italic">Pish</Emphasis> introgression

Rice blast is a serious disease caused by the filamentous ascomycetous fungus Magnaporthe oryzae. Incorporating disease resistance genes in rice varieties and characterizing the distribution of M. oryzae isolates form the foundation for enhancing rice blast resistance. In this study, the blast resistance gene Pish was observed to be differentially distributed in the genomes of rice sub-species. Specifically, Pish was present in 80.5% of Geng varieties, but in only 2.3% of Xian varieties. Moreover, Pish conferred resistance against only 23.5% of the M. oryzae isolates from the Geng-planting regions, but against up to 63.2% of the isolates from the Xian-planting regions. Thus, Pish may be an elite resistance gene for improving rice blast resistance in Xian varieties. Therefore, near-isogenic lines (NILs) with Pish and the polygene pyramid lines (PPLs) PPL^Pish/Pi1, PPL^Pish/Pi54, and PPL^Pish/Pi33 in the Xian background Yangdao 6 were generated using a molecular marker-assisted selection method. The results suggested that (1) Pish significantly improved rice blast resistance in Xian varieties, which exhibited considerably improved seedling and panicle blast resistance after Pish was introduced; (2) PPLs with Pish were more effective than the NILs with Pish regarding seedling and panicle blast resistance; (3) the PPL seedling and panicle blast resistance was improved by the complementary and overlapping effects of different resistance genes; and (4) the stability of NIL and PPL resistance varied under different environmental conditions, with only PPL^Pish/Pi54 exhibiting highly stable resistance in three natural disease nurseries (Jianyang, Jinggangshan, and Huangshan). This study provides new blast resistance germplasm resources and describes a novel molecular strategy for enhancing rice blast resistance.     

Development of near-isogenic lines with different alleles of Piz locus and analysis of their breeding effect under Yangdao 6 background

Rice blast is one of the most destructive diseases of rice. The most effective way of managing this disease is to develop resistant cultivars by introducing resistance genes into elite rice recipients. In this study, the near-isogenic lines (NILs) of six resistance alleles of the Piz locus (Pizt, Pi2, Pigm, Pi40, Pi9 and Piz) were constructed with Yangdao 6 as genetic background. Seedling inoculation tests showed that most of the NILs, namely NIL-Pi2, NIL-Pigm, NIL-Pi9, NIL-Pizt and NIL-Pi40, exhibited good resistance to blast with resistance frequencies (RFs) of over 82.50 %, execpt NIL-Piz which showed lower resistance with a RF of only 36.13 %. Furthermore, the improved-resistance NILs exhibited high similarity of their resistance spectra, with overlapping degrees of resistance spectrum (OD) of more than 75.83 %. However, the RF of panicle blast for all NILs decreased significantly compared with seedling blast in an artificial inoculation test. Although NIL-Pigm showed a higher panicle blast RF of 80 %, other NILs with outstanding performance in seedling blast resistance, namely NIL-Pizt, NIL-Pi2, NIL-Pi9 and NIL-Pi40, exhibited middle or low RFs of panicle blast with values from 56.67 to 33.30 %. Natural induction in a disease nursery showed a consistent trend in artificial inoculation results at seedling and heading stages. While NIL-Pigm was found to exhibit good resistance to leaf blast and panicle blast, NIL-Pi9 and NIL-Pizt were further demonstrated to show excellent resistance in Suichuan, Jiangxi province and Enshi, Hubei province, respectively, because of the race–region specificity. Agronomic traits of NILs were also investigated in order to evaluate the linkage drag effect of different alleles of the Piz locus. The resistance effects of the different alleles of the Piz locus under identical genetic background against seedling blast and panicle blast was first reported in this study, and the above results are expected to provide a theoretical support for the rational utilization of broad-spectrum resistance genes in breeding practice.     

Temperature-dependent QTLs in <Emphasis Type="Italic">indica</Emphasis> alleles for improving grain quality in rice: increased prominence of QTLs responsible for reduced chalkiness under high-temperature conditions

Quantitative trait loci (QTLs) for the apparent quality of brown rice under high temperatures during ripening were analyzed using chromosomal segment substitution lines. Segments from the indica cultivar Habataki were substituted into a japonica cultivar with a Sasanishiki background. We found the following two QTLs for increasing grain quality in the Habataki allele on chromosome 3: (1) qTW3-2, located near the marker RM14702, decreased the percentage of total white immature (TWI) grains, and (2) qRG3-2, located near RM3766, increased the percentage of regular grains. The effects of these two QTLs were more obvious under high-temperature ripening conditions; hence, these loci are considered QTLs not only for reducing TWI grains but also for increasing high-temperature tolerance. Additionally, we found two QTLs, i.e., qTW3-1 and qRG3-1, responsible for reduced grain quality near RM14314 on chromosome 3. Although the QTL for narrow grains in the Habataki allele qNG3 was genetically linked to qTW3-2, the effect was only slightly significant, and the length/width ratio of qNG3-carrying grains was within the range observed in widely grown japonica cultivars. Incorporating the Habataki region, including qRG3-2 and qTW3-2 but not qTW3-1 and qRG3-1, in addition to previously reported grain quality QTLs in breeding japonica cultivars will improve high-temperature tolerance and grain quality.     

A novel QTL <Emphasis Type="Italic">qSPP2.2</Emphasis> controlling spikelet per panicle identified from <Emphasis Type="Italic">Oryza longistaminata</Emphasis> (A. Chev. et Roehr.), mapped and transferred to <Emphasis Type="Italic">Oryza sativa</Emphasis> (L.)

Increasing the rice productivity from the current 10 to 12 tons/ha to meet the demand of estimated 8.8 billion people in 2035 is posing a major challenge. Wild relatives of rice contain some novel genes which can help in improving rice yield. Spikelet per panicle (SPP) is a valuable trait for determining yield potential in rice. In this study, a major QTL for increasing SPP has been identified, mapped, and transferred from African wild rice O. longistaminata to O. sativa (L.). The QTL was mapped on the long arm of chromosome 2 in a 167.1 kb region flanked by SSR markers RM13743 and RM13750, which are 1.0 cM apart, and is designated as qSPP2.2. The QTL explained up to 30% of phenotypic variance in different generations/seasons and showed positive additive effect of allele contributed by O. longistaminata. In addition, O. longistaminata allele in qSPP2.2 contributed to increase in grains per panicle, but decrease in the tillers per plant. The 167.1 kb region contains 23 predicted genes. Based on the functional annotation, three genes, LOC_Os02g44860, LOC_Os02g44990, and LOC_Os02g45010, were selected as putative candidates for characterization. Sequence analysis of the three genes revealed functional variations between the parental lines for LOC_Os02g44990 and a variation in 5′UTR for LOC_Os02g45010 which will help further to identify putative candidate gene(s). This is the first yield component QTL to be identified, mapped, and transferred from O. longistaminata.     

Assessment of genetic diversity of <Emphasis Type="Italic">Saltol</Emphasis> QTL among the rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.) genotypes

Eight Saltol quantitative trait locus (QTL) linked simple sequence repeat (SSR) markers of rice (Oryza sativa L.) were used to study the polymorphism of this QTL in 142 diverse rice genotypes that comprised salt tolerant as well as sensitive genotypes. The SSR profiles of the eight markers generated 99 alleles including 20rare alleles and 16 null alleles. RM8094 showed the highest number (13) of alleles followed by RM3412 (12), RM562 (11), RM493 (9) and RM1287 (8) while as, RM10764 and RM10745 showed the lowest number (6) of alleles. Based on the highest number of alleles and PIC value (0.991), we identified RM8094 as suitable marker for discerning salt tolerant genotypes from the sensitive ones. Based upon the haplotype analysis using FL478 as a reference (salt tolerant genotypes containing Saltol QTL), we short listed 68 rice genotypes that may have at least one allele of FL478 haplotype. Further study may confirm that some of these genotypes might have Saltol QTL and can be used as alternative donors in salt tolerant rice breeding programmes.     

High-resolution mapping of genes involved in plant stage-specific partial resistance of barley to leaf rust

Partial resistance quantitative trait loci (QTLs) Rphq11 and rphq16 against Puccinia hordei isolate 1.2.1 were previously mapped in seedlings of the mapping populations Steptoe/Morex and Oregon Wolfe Barleys, respectively. In this study, QTL mapping was performed at adult plant stage for the two mapping populations challenged with the same rust isolate. The results suggest that Rphq11 and rphq16 are effective only at seedling stage, and not at adult plant stage. The cloning of several genes responsible for partial resistance of barley to P. hordei will allow elucidation of the molecular basis of this type of plant defence. A map-based cloning approach requires to fine-map the QTL in a narrow genetic window. In this study, Rphq11 and rphq16 were fine-mapped using an approach aiming at speeding up the development of plant material and simplifying its evaluation. The plant materials for fine-mapping were identified from early plant materials developed to produce QTL-NILs. The material was first selected to carry the targeted QTL in heterozygous condition and susceptibility alleles at other resistance QTLs in homozygous condition. This strategy took four to five generations to obtain fixed QTL recombinants (i.e., homozygous resistant at the Rphq11 or rphq16 QTL alleles, homozygous susceptible at the non-targeted QTL alleles). In less than 2 years, Rphq11 was fine-mapped into a 0.2-cM genetic interval and a 1.4-cM genetic interval for rphq16. The strongest candidate gene for Rphq11 is a phospholipid hydroperoxide glutathione peroxidase. Thus far, no candidate gene was identified for rphq16.     

Identification of novel recessive gene <Emphasis Type="Italic">xa44</Emphasis>(<Emphasis Type="Italic">t</Emphasis>) conferring resistance to bacterial blight races in rice by QTL linkage analysis using an SNP chip

Key message

Using QTL analysis and fine mapping, the novel recessive gene xa44(t) conferring resistance to BB was identified and the expression level of the gene was confirmed through qRT-PCR analysis.

Abstract

Bacterial blight (BB) disease caused by Xanthomonas oryzae pv. oryzae (Xoo) is a major factor causing rice yield loss in most rice-cultivating countries, especially in Asia. The deployment of cultivars with resistance to BB is the most effective method to control the disease. However, the evolution of new Xoo or pathotypes altered by single-gene-dependent mutations often results in breakdown of resistance. Thus, efforts to identify novel R-genes with sustainable BB resistance are urgently needed. In this study, we identified three quantitative trait loci (QTLs) on chromosomes 1, 4, and 11, from an F₂ population of 493 individuals derived from a cross between IR73571-3B-11-3-K3 and Ilpum using a 7K SNP chip. Of these QTLs, one major QTL, qBB_11, on chromosome 11 explained 61.58% of the total phenotypic variance in the population, with an LOD value of 113.59, based on SNPs 11964077 and 11985463. The single major R-gene, with recessive gene action, was designated xa44(t) and was narrowed down to a 120-kb segment flanked within 28.00 Mbp to 28.12 Mbp. Of nine ORFs present in the target region, two ORFs revealed significantly different expression levels of the candidate genes. These candidate genes (Os11g0690066 and Os11g0690466) are described as “serine/threonine protein kinase domain containing protein” and “hypothetical protein,” respectively. The results will be useful to further understand BB resistance mechanisms and provide new sources of resistance, together with DNA markers for MAS breeding to improve BB resistance in rice.

     

QTL mapping for downy mildew resistance in cucumber via bulked segregant analysis using next-generation sequencing and conventional methods

Key message

QTL mapping using NGS-assisted BSA was successfully applied to an F ₂ population for downy mildew resistance in cucumber. QTLs detected by NGS-assisted BSA were confirmed by conventional QTL analysis.

Abstract

Downy mildew (DM), caused by Pseudoperonospora cubensis, is one of the most destructive foliar diseases in cucumber. QTL mapping is a fundamental approach for understanding the genetic inheritance of DM resistance in cucumber. Recently, many studies have reported that a combination of bulked segregant analysis (BSA) and next-generation sequencing (NGS) can be a rapid and cost-effective way of mapping QTLs. In this study, we applied NGS-assisted BSA to QTL mapping of DM resistance in cucumber and confirmed the results by conventional QTL analysis. By sequencing two DNA pools each consisting of ten individuals showing high resistance and susceptibility to DM from a F₂ population, we identified single nucleotide polymorphisms (SNPs) between the two pools. We employed a statistical method for QTL mapping based on these SNPs. Five QTLs, dm2.2, dm4.1, dm5.1, dm5.2, and dm6.1, were detected and dm2.2 showed the largest effect on DM resistance. Conventional QTL analysis using the F₂ confirmed dm2.2 (R ² = 10.8–24 %) and dm5.2 (R ² = 14–27.2 %) as major QTLs and dm4.1 (R ² = 8 %) as two minor QTLs, but could not detect dm5.1 and dm6.1. A new QTL on chromosome 2, dm2.1 (R ² = 28.2 %) was detected by the conventional QTL method using an F₃ population. This study demonstrated the effectiveness of NGS-assisted BSA for mapping QTLs conferring DM resistance in cucumber and revealed the unique genetic inheritance of DM resistance in this population through two distinct major QTLs on chromosome 2 that mainly harbor DM resistance.

     

Characterisation of a novel quantitative trait locus, <Emphasis Type="Italic">GN4</Emphasis>-<Emphasis Type="Italic">1</Emphasis>, for grain number and yield in rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.)

Key message

A novel QTL for grain number, GN4-1, was identified and fine-mapped to an ~ 190-kb region on the long arm of rice chromosome 4.

Abstract

Rice grain yield is primarily determined by three components: number of panicles per plant, grain number per panicle and grain weight. Among these traits, grain number per panicle is the major contributor to grain yield formation and is a crucial trait for yield improvement. In this study, we identified a major quantitative trait locus (QTL) responsible for rice grain number on chromosome 4, designated GN4-1 (a QTL for Grain Number on chromosome 4), using advanced segregating populations derived from the crosses between an elite indica cultivar ‘Zhonghui 8006’ (ZH8006) and a japonica rice ‘Wuyunjing 8’ (WYJ8). GN4-1 was delimited to an ~ 190-kb region on chromosome 4. The genetic effect of GN4-1 was estimated using a pair of near-isogenic lines. The GN4-1 gene from WYJ8 promoted accumulation of cytokinins in the inflorescence and increased grain number per panicle by ~ 17%. More importantly, introduction of the WYJ8 GN4-1 gene into ZH8006 increased grain yield by ~ 14.3 and ~ 11.5% in the experimental plots in 2014 and 2015, respectively. In addition, GN4-1 promoted thickening of the culm and may enhance resistance to lodging. These results demonstrate that GN4-1 is a potentially valuable gene for improvement of yield and lodging resistance in rice breeding.

     

Identification and fine mapping of <Emphasis Type="Italic">qWBPH11</Emphasis> conferring resistance to whitebacked planthopper (<Emphasis Type="Italic">Sogatella furcifera</Emphasis> Horvath) in rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.)

The whitebacked planthopper (WBPH), Sogatella furcifera Horvath, is one of the most destructive pests in rice (Oryza sativa L.) production. Host-plant resistance has been considered as an efficient and eco-friendly strategy to reduce yield losses caused by WBPH. In this study, we found that an indica rice cultivar IR54751-2-44-15-24-2 (IR54751) displayed high resistance to WBPH at both seedling and tillering stages. The resistance of IR54751 was mainly contributed by antixenosis and tolerance rather than antibiosis. An F₂ population derived from a cross between IR54751 and a susceptible japonica cultivar 02428 was constructed to detect the quantitative trait loci (QTLs) conferring the resistance to WBPH. In total, four QTLs including qWBPH3.1, qWBPH3.2, qWBPH11, and qWBPH12 were identified and distributed on three different chromosomes. The four QTLs had LOD scores of 3.8, 8.2, 5.8, and 3.9, accounting for 8.2, 21.5, 13.9, and 10.4% of the phenotypic variation, respectively. Except for qWBPH3.1, the resistance alleles of the other three QTLs were all from IR54751. Further, a secondary population harboring only single qWBPH11 locus was developed from the F₂ population by marker-assisted selection. Finally, qWBPH11 was delimited in a 450-kb region between markers DJ53973 and SNP56. The identification of WBPH resistance QTLs and the fine mapping of qWBPH11 will be helpful for cloning resistance genes and breeding resistant rice cultivars.     

Molecular mapping of QTL for Fusarium head blight resistance introgressed into durum wheat

Key message

The major QTL for FHB resistance from hexaploid wheat line PI 277012 was successfully introgressed into durum wheat and minor FHB resistance QTL were detected in local durum wheat cultivars. A combination of these QTL will enhance FHB resistance of durum wheat.

Abstract

Fusarium head blight (FHB), caused by Fusarium graminearum, is a devastating disease of durum wheat. To combat the disease, great efforts have been devoted to introgress FHB resistance from its related tetraploid and hexaploid wheat species into adapted durum cultivars. However, most of the quantitative trait loci (QTL) for FHB resistance existing in the introgression lines are not well characterized or validated. In this study, we aimed to identify and map FHB resistance QTL in a population consisting of 205 recombinant inbred lines from the cross between Joppa (a durum wheat cultivar) and 10Ae564 (a durum wheat introgression line with FHB resistance derived from the hexaploid wheat line PI 277012). One QTL (Qfhb.ndwp-2A) from Joppa and two QTL (Qfhb.ndwp-5A and Qfhb.ndwp-7A) from 10Ae564 were identified through phenotyping of the mapping population for FHB severity and DON content in greenhouse and field and genotyping with 90K wheat Infinium iSelect SNP arrays. Qfhb.ndwp-2A explained 14, 15, and 9% of the phenotypic variation, respectively, for FHB severity in two greenhouse experiments and for mean DON content across the two greenhouse environments. Qfhb.ndwp-5A explained 19, 10, and 7% of phenotypic variation, respectively, for FHB severity in one greenhouse experiment, mean FHB severity across two field experiments, and mean DON content across the two greenhouse experiments. Qfhb.ndwp-7A was only detected for FHB severity in the two greenhouse experiments, explaining 9 and 11% of the phenotypic variation, respectively. This study confirms the existence of minor QTL in North Dakota durum cultivars and the successful transfer of the major QTL from PI 277012 into durum wheat.

     

QTL mapping of Fusarium head blight resistance in three related durum wheat populations

Key message

The QTL Fhb1 was successfully introgressed and validated in three durum wheat populations. The novel germplasm and the QTL detected will support improvement of Fusarium resistance in durum wheat.

Abstract

Durum wheat (Triticum durum Desf.) is particularly susceptible to Fusarium head blight (FHB) and breeding for resistance is hampered by limited genetic variation within this species. To date, resistant sources are mainly available in a few wild relative tetraploid wheat accessions. In this study, the effect of the well-known hexaploid wheat (Triticum aestivum L.) quantitative trait locus (QTL) Fhb1 was assessed for the first time in durum wheat. Three F7-RIL mapping populations of about 100 lines were developed from crosses between the durum wheat experimental line DBC-480, which carries an Fhb1 introgression from Sumai-3, and the European T. durum cultivars Karur, Durobonus and SZD1029K. The RILs were evaluated in field experiments for FHB resistance in three seasons using spray inoculation and genotyped with SSR as well as genotyping-by-sequencing markers. QTL associated with FHB resistance were identified on chromosome arms 2BL, 3BS, 4AL, 4BS, 5AL and 6AS at which the resistant parent DBC-480 contributed the positive alleles. The QTL on 3BS was detected in all three populations centered at the Fhb1 interval. The Rht-B1 locus governing plant height was found to have a strong effect in modulating FHB severity in all populations. The negative effect of the semi-dwarf allele Rht-B1b on FHB resistance was compensated by combining with Fhb1 and additional resistance QTL. The successful deployment of Fhb1 in T. durum was further substantiated by assessing type 2 resistance in one population. The efficient introgression of Fhb1 represents a significant step forward for enhancing FHB resistance in durum wheat.

     

Evaluation of QTLs for Shoot Fly (<Emphasis Type="Italic">Atherigona soccata</Emphasis>) Resistance Component Traits of Seedling Leaf Blade Glossiness and Trichome Density on Sorghum (<Emphasis Type="Italic">Sorghum bicolor</Emphasis>) Chromosome SBI-10L

Shoot fly is a major insect pest of sorghum damaging early crop growth, establishment and productivity. Host plant resistance is an efficient approach to minimize yield losses due to shoot fly infestation. Seedling leaf blade glossiness and trichome density are morphological traits associated with shoot fly resistance. Our objective was to identify and evaluate QTLs for glossiness and trichome density using- i) 1894 F₂s, ii) a sub-set of 369 F₂-recombinants, and iii) their derived 369 F_2:3 progenies, from a cross involving introgression lines RSG04008-6 (susceptible)?×?J2614-11 (resistant). The QTLs were mapped to a 37–72 centimorgan (cM) or 5–15 Mb interval on the long arm of sorghum chromosome 10 (SBI-10L) with flanking markers Xgap001 and Xtxp141. One QTL each for glossiness (QGls10) and trichome density (QTd10) were mapped in marker interval Xgap001-Xnhsbm1044 and Xisep0630-Xtxp141, confirming their loose linkage, for which phenotypic variation accounted for ranged from 2.29 to 11.37 % and LOD values ranged from 2.03 to 24.13, respectively. Average physical map positions for glossiness and trichome density QTLs on SBI-10 from earlier studies were 4 and 2 Mb, which in the present study were reduced to 2 Mb and 800 kb, respectively. Candidate genes Glossy15 (Sb10g025053) and ethylene zinc finger protein (Sb10g027550) falling in support intervals for glossiness and trichome density QTLs, respectively, are discussed. Also we identified a sub-set of recombinant population that will facilitate further fine mapping of the leaf blade glossiness and trichome density QTLs on SBI-10.     

Identification and mapping of resistance to stem rust in the European winter wheat cultivars Spark and Rialto

A mapping population of 126 doubled haploid (DH) lines derived from a cross between the English winter wheat cultivars Spark and Rialto was evaluated for response to Puccinia graminis f. sp. tritici in the greenhouse and in artificially inoculated field plots at two locations over 3 years (2011, 2012 and 2013). Genetic analysis indicated the involvement of two seedling genes (Sr5 and Sr31, contributed by Rialto) and three adult plant resistance genes. QTL analyses of field data showed the involvement of three consistent effects QTL on chromosome arms 1BS (contributed by Rialto), and 3BS and chromosome 5A (contributed by Spark) in the observed resistance to stem rust. These QTLs explained average phenotypic variation of 78.5, 9.0 and 5.9 %, respectively. With the presence of virulence for Sr5 and absence of Sr31 virulence in the field, the QTL detected on 1BS (QSr.sun-1BS) was attributed to the major seedling resistance gene Sr31. The QTL located on chromosome arm 3BS (QSr.sun-3BS) was closely associated with SSR marker gwm1034, and the QTL detected on 5A (QSr.sun-5A) was closely linked with SSR marker gwm443. DH lines carrying the combination of QSr.sun-3BS and QSr.sun-5A exhibited lower stem rust responses indicating the additive effects of the two APR genes in reducing disease severity. The markers identified in this study can be useful in pyramiding these QTLs with other major or minor genes and marker assisted selection for stem rust resistance in wheat.     

Identification and pyramiding of QTLs for cold tolerance at the bud bursting and the seedling stages by use of single segment substitution lines in rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.)

Cold stress is one of the main constraints in rice production, and damage from cold can occur at different developmental stages in rice. Understanding the genetic basis of cold tolerance is the key for breeding cold-tolerant variety. In this study, we used single segment substitution lines (SSSLs) derived from a cross between cold-tolerant japonica variety “Nan-yang-zhan” and a popular indica variety “Hua-jing-xian 74” to detect and pyramid QTLs for cold tolerance at the bud bursting and the seedling stages. Evaluation of cold tolerance of these SSSLs and their recurrent parent helped identify two cold-tolerant QTLs (qCTBB-5 and qCTBB-6) at the bud bursting stage and two cold-tolerant QTLs (qCTS-6 and qCTS-12) at the seedling stage. The SSSLs carrying these QTLs showed stronger cold tolerance than their recurrent parent HJX74 did in three independent experiments. The qCTBB-6 and qCTS-6 were mapped to the same chromosomal region. QTL pyramiding was performed by intercrossing of SSSLs carrying the respective QTLs for cold tolerance at the bud bursting stage and the seedling stage and marker-assisted selection (MAS). The selected pyramiding line SC1-1 with different cold-tolerant QTLs showed cumulative effects on cold tolerance. Our results suggest that different genes (QTLs) control cold tolerance at bud bursting and seedling stages, and pyramiding of stable expression QTLs for cold tolerance at different developmental stages through MAS is a good strategy to prevent cold damage in rice.     

QTLs for heading date and plant height under multiple environments in rice

Both heading date and plant height are important traits related to grain yield in rice. In this study, a recombinant inbred lines (RILs) population was used to map quantitative trait loci (QTLs) for both traits under 3 long-day (LD) environments and 1 short-day (SD) environment. A total of eight QTLs for heading date and three QTLs for plant height were detected by composite interval mapping under LD conditions. Additional one QTL for heading date and three QTLs for plant height were identified by Two-QTL model under LD conditions. Among them, major QTLs qHd7.1, qHd7.2 and qHd8 for heading date, and qPh1 and qPh7.1 for plant height were commonly detected. qHd7.1 and qHd7.2 were mapped to small regions of less than 1 cM. Genome position comparison of previously cloned genes with QTLs detected in this study revealed that qHd5 and qPh3.1 were two novel QTLs. The alleles of these QTLs increasing trait values were dispersed in both parents, which well explained the transgressive segregation observed in this population. In addition, the interaction between qHd7.1 and qHd8 was detected under all LD conditions. Multiple-QTL model analysis revealed that all QTLs and their interactions explained over 80% of heading date variation and 50% of plant height variation. Two heading date QTLs were detected under SD condition. Of them, qHd10 were commonly identified under LD condition. The difference in QTL detection between LD and SD conditions indicated most heading date QTLs are sensitive to photoperiod. These findings will benefit breeding design for heading date and plant height in rice.     

Development and characterization of <Emphasis Type="Italic">Brassica juncea – fruticulosa</Emphasis> introgression lines exhibiting resistance to mustard aphid (<Emphasis Type="Italic">Lipaphis erysimi</Emphasis> Kalt)

Background

Mustard aphid is a major pest of Brassica oilseeds. No source for aphid resistance is presently available in Brassica juncea . A wild crucifer, Brassica fruticulosa is known to be resistant to mustard aphid. An artificially synthesized amphiploid, AD-4 (B. fruticulosa × B. rapa var. brown sarson) was developed for use as a bridge species to transfer fruticulosa resistance to B. juncea. Using the selfed backcross we could select a large number of lines with resistance to mustard aphid. This paper reports cytogenetic stability of introgression lines, molecular evidence for alien introgression and their reaction to mustard aphid infestation.

Results

Majority of introgression lines had expected euploid chromosome number(2n= 36), showed normal meiosis and high pollen grain fertility. Well-distributed and transferable simple-sequence repeats (SSR) markers for all the 18 B. juncea chromosomes helped to characterize introgression events. Average proportions of recipient and donor genome in the substitution lines were 49.72 and 35.06%, respectively. Minimum alien parent genome presence (27.29%) was observed in the introgression line, Ad3K-280 . Introgressed genotypes also varied for their resistance responses to mustard aphid infestations under artificial release conditions for two continuous seasons. Some of the test genotypes showed consistent resistant reaction.

Conclusions

B.juncea-fruticulosa introgression set may prove to be a very powerful breeding tool for aphid resistance related QTL/gene discovery and fine mapping of the desired genes/QTLs to facilitate marker assisted transfer of identified gene(s) for mustard aphid resistance in the background of commercial mustard genotypes.