Molecular mapping of Fusarium head blight resistance in the winter wheat population Dream/Lynx

Fusarium head blight (FHB), mainly caused by Fusarium graminearum and F. culmorum, can significantly reduce the grain quality of wheat (Triticum aestivum L.) due to mycotoxin contamination. The objective of this study was to identify quantitative trait loci (QTLs) for FHB resistance in a winter wheat population developed by crossing the resistant German cultivar Dream with the susceptible British cultivar Lynx. A total of 145 recombinant inbred lines (RILs) were evaluated following spray inoculation with a F. culmorum suspension in field trials in 2002 in four environments across Germany. Based on amplified fragment length polymorphism and simple sequence repeat marker data, a 1,734 cM linkage map was established assuming that the majority of the polymorphic parts of the genome were covered. The area under disease progress curve (AUDPC) was calculated based on the visually scored FHB symptoms. The population segregated quantitatively for FHB severity. Composite interval mapping analysis for means across the environments identified four FHB resistance QTLs on chromosomes 6AL, 1B, 2BL and 7BS. Individually the QTLs explained 19%, 12%, 11% and 21% of the phenotypic variance, respectively, and together accounted for 41%. The QTL alleles conferring resistance on 6AL, 2BL and 7BS originated from cv. Dream. The resistance QTL on chromosome 6AL partly overlapped with a QTL for plant height. The FHB resistance QTL on 7BS coincided with a QTL for heading date, but the additive effect on heading date was of minor importance. The resistance QTL on chromosome 1B was associated with the T1BL.1RS wheat-rye translocation of Lynx.     

Mapping of QTLs conferring extremely early heading in rice (Oryza sativa L.)

Two genes related to extremely early heading were identified in populations derived from crosses between Hoshinoyume, a variety adapted to the northernmost limit of rice cultivation (Hokkaido), and Nipponbare, a variety adapted to the temperate region of Japan. The segregations for heading date clearly revealed that a two-gene model determined the extremely early heading in the F₂ and BC₁F₁ populations under natural field conditions in Hokkaido. Using molecular markers corresponding to ten known quantitative trait loci (QTLs) for heading date, we carried out QTL analysis in the BC₁F₁ population and detected two QTLs, qDTH-7-1 and qDTH-7-2, both on chromosome 7, and observed epistatic interaction between them. We conclude that the recessive alleles of these two genes contribute to extremely early heading for the adaptation to Hokkaido environment and to stable rice production in Hokkaido. The relationships between the two QTLs identified in this study and known QTLs are discussed.     

Mapping quantitative trait loci controlling seed dormancy and heading date in rice, Oryza sativa L., using backcross inbred lines

 To detect quantitative trait loci (QTLs) controlling seed dormancy, 98 BC₁F₅ lines (backcross inbred lines) derived from a backcross of Nipponbare (japonica)/Kasalath (indica)//Nipponbare were analyzed genetically. We used 245 RFLP markers to construct a framework linkage map. Five putative QTLs affecting seed dormancy were detected on chromosomes 3, 5, 7 (two regions) and 8, respectively. Phenotypic variations explained by each QTL ranged from 6.7% to 22.5% and the five putative QTLs explained about 48% of the total phenotypic variation in the BC₁F₅ lines. Except for those of the QTLs on chromosome 8, the Nipponbare alleles increased the germination rate. Five putative QTLs controlling heading date were detected on chromosomes 2, 3, 4, 6 and 7, respectively. The phenotypic variation explained by each QTL for heading date ranged from 5.7% to 23.4% and the five putative QTLs explained about 52% of the total phenotypic variation. The Nipponbare alleles increased the number of days to heading, except for those of two QTLs on chromosomes 2 and 3. The map location of a putative QTL for heading date coincided with that of a major QTL for seed dormancy on chromosome 3, although two major heading-date QTLs did not coincide with any seed dormancy QTLs detected in this study. Received: 10 October 1997 / Accepted: 12 January 1998     

Uncovering of major genetic factors generating naturally occurring variation in heading date among Asian rice cultivars

To dissect the genetic factors controlling naturally occurring variation of heading date in Asian rice cultivars, we performed QTL analyses using F₂ populations derived from crosses between a japonica cultivar, Koshihikari, and each of 12 cultivars originating from various regions in Asia. These 12 diverse cultivars varied in heading date under natural field conditions in Tsukuba, Japan. Transgressive segregation was observed in 10 F₂ combinations. QTL analyses using multiple crosses revealed a comprehensive series of loci involved in natural variation in flowering time. One to four QTLs were detected in each cross combination, and some QTLs were shared among combinations. The chromosomal locations of these QTLs corresponded well with those detected in other studies. The allelic effects of the QTLs varied among the cross combinations. Sequence analysis of several previously cloned genes controlling heading date, including Hd1, Hd3a, Hd6, RFT1, and Ghd7, identified several functional polymorphisms, indicating that allelic variation at these loci probably contributes to variation in heading date. Taken together, the QTL and sequencing results indicate that a large portion of the phenotypic variation in heading date in Asian rice cultivars could be generated by combinations of different alleles (possibly both loss- and gain-of-function) of the QTLs detected in this study.     

Additive and additive x additive interaction make important contributions to spikelets per panicle in rice near isogenic （Oryza sativa L.） lines

Epistasis plays an important role in the genetic basis of rice yield traits. Taking interactions into account in breeding programs will help the development of high-yielding rice varieties. In this study, three sets of near isogenic lines (NILs) targeting three QTLs for spikelets per panicle (SPP), namely qSPP1, qSPP2 and qSPP7, which share the same Zhenshan 97 genetic background, were used to produce an F₂ population in which the three QTLs segregated simultaneously. The genotypes of the individual F₂ plants at the three QTLs were replaced with three markers that are closely linked to the corresponding QTLs. These QTLs were validated in the F₂ and F₃ populations at the single marker level. qSPP7 exhibited major pleiotropic effects on SPP, plant height and heading date. Multifactor analysis of variance was performed for the F₂ population and its progeny. Additive (additive interaction between qSPP2 and qSPP7 had significant effects on SPP in both the F₂ population and its progeny. Both additive and additive (additive interactions could explain about 73% of the total SPP phenotypic variance. The SPP performance of 27 three-locus combinations was ranked and favorable combinations were recommended for rice breeding in different ecosystems.     

Chromosomal location of genomic SSR markers associated with yellow rust resistance in Turkish bread wheat (Triticum aestivum L.)

We have previously reported Xgwm382 as a diagnostic marker for disease resistance against yellow rust in Izgi2001 × ES14 F₂ population. Among the same earlier tested 230 primers, one SSR marker (Xgwm311) also amplified a fragment which is present in the resistant parent and in the resistant bulks, but absent in the susceptible parent and in the susceptible bulks. To understand the chromosome group location of these diagnostic markers, Xgwm382 and Xgwm311, in the same population, we selected 16 SSR markers mapped only in one genome of chromosome group 2 around 1–21 cM distance to these diagnostic markers based on the SSR consensus map of wheat. Out of 16 SSRs, Xwmc658 identified resistant F₂ individuals as a diagnostic marker for yellow rust disease and provided the location of Xgwm382 and Xgwm311 on chromosome 2AL in our plant material.     

Fine mapping of qHd1, a minor heading date QTL with pleiotropism for yield traits in rice (Oryza sativa L.)

Key message

A minor QTL for heading date located on the long arm of rice chromosome 1 was delimitated to a 95.0-kb region using near isogenic lines with sequential segregating regions.

Abstract

Heading date and grain yield are two key factors determining the commercial potential of a rice variety. In this study, rice populations with sequential segregating regions were developed and used for mapping a minor QTL for heading date, qHd1. A total of 18 populations in six advanced generations through BC₂F₆ to BC₂F₁₁ were derived from a single BC₂F₃ plant of the indica rice cross Zhenshan 97 (ZS97)///ZS97//ZS97/Milyang 46. The QTL was delimitated to a 95.0-kb region flanked by RM12102 and RM12108 in the terminal region of the long arm of chromosome 1. Results also showed that qHd1 was not involved in the photoperiodic response, having an additive effect ranging from 2.4 d to 2.9 d observed in near isogenic lines grown in the paddy field and under the controlled conditions of either short day or long day. The QTL had pleiotropic effects on yield traits, with the ZS97 allele delaying heading and increasing the number of spikelets per panicle, the number of grains per panicle and grain yield per plant. The candidate region contains ten annotated genes including two genes with functional information related to the control of heading date. These results lay a foundation for the cloning of qHd1. In addition, this kind of minor QTLs could be of great significance in rice breeding for allowing minor adjustment of heading date and yield traits.     

Detection of QTLs for heading time and photoperiod response in wheat using a doubled-haploid population.

The genetic basis of heading time in wheat (Triticum aestivum L.) was investigated through the study of flowering under normal autumn sown field conditions as well as photoperiod responses under a controlled environment. Quantitative trait loci (QTLs) for these traits were mapped in a doubled-haploid (DH) population derived from a cross between the wheat cultivars 'Courtot' and 'Chinese Spring'. A molecular marker linkage map of this cross that was previously constructed based on 187 DH lines and 380 markers was used for QTL mapping. The genome was well covered (85%) except for chromosomes 1D and 4D, and a set of anchor loci regularly spaced over the genome (one marker each 15.5 cM) was chosen for marker regression analysis. The presence of a QTL was declared at a significance threshold of alpha = 0.005. The population was grown under field conditions in Clermont-Ferrand, France during two years (1994-1995), in Norwich, U.K. over one year (1998), and also under controlled environments in Norwich. For each trait, between 2 and 4 QTLs were identified with individual effects ranging between 6.3% and 44.4% of the total phenotypic variation. Two QTLs were detected that simultaneously affected heading time and photoperiod response. For heading time, these two QTLs were detected in more than one year. One QTL located on chromosome arm 2BS near the locus Xfbb121-2B, co-segregated with the gene Ppd-B1 known to be involved in photoperiod response. This chromosome region explained a large part of the variation (23.4-44.4% depending on the years or the traits). Another region located on chromosome arm 7BS between the loci Xfbb324-7B and Xfbb53-7B also had a strong effect (7.3-15.3%). This region may correspond to a QTL for earliness per se.     

Identification of quantitative trait loci and epistatic interactions for plant height and heading date in rice

Appropriate heading date and plant height are prerequisites for attaining the desired yield level in rice breeding programs. In this study, we analyzed the genetic bases of heading date and plant height at both single- locus and two-locus levels, using a population of 240 F_2:3 families derived from a cross between two elite rice lines. Measurements for the traits were obtained over 2 years in replicated field trials. A linkage map was constructed with 151 polymorphic marker loci, based on which interval mapping was performed using Mapmaker/QTL. The analyses detected six QTLs for plant height and six QTLs for heading date; collectively the QTLs for heading date accounted for a much greater amount of phenotypic variation than did the QTLs for plant height. Two-way analyses of variance, with all possible two-locus combinations, detected large numbers (from 101 to 257) of significant digenic interactions in the 2 years for both traits involving markers distributed in the entire genome; 22 and 39 were simultaneously detected in both years for plant height and heading date, respectively. Each of the interactions individually accounted for only a very small portion of the phenotypic variation. The majority of the significant interactions involved marker loci that did not detect significant effects by single-locus analyses, and many of the QTLs detected by single-locus analyses were involved in epistatic interactions. The results clearly demonstrated the importance of epistatic interactions in the genetic bases of heading date and plant height. Received: 5 May 2001 / Accepted: 3 August 2001     

水稻F2不育和抽穗期QTL分析

对台中65（粳稻）/Bhadua（籼稻）杂交F2代群体构建了RFLP连锁图谱,含94个分布较为均匀的标记。对F2小穗不育性状进行单点分析和区间分析的结果基本一致：有两个F2小穗不育QTL座位分别位于染色体1的XNpb113～XNpb346之间和染色体8的G187～XNpb397之间,而且该两个QTL均为新检测出的座位;检测出5个抽穗期TQL,其中3个座位在单点分析和区间分析中的结果一致,分别位于染色体1的XNpb113～XNpb346,染色体4的C891～C335,染色体的8的C166～C1121,另外,染色体6的XNpb27为单点分析结果,染色体10的R716～C405为区间分析结果。由于染色体1上的F2不育QTL和抽穗期QTL重叠,该QTL座位是由于遗传效应所至还是由于环境因素（迟抽穗）所至有待构建近等基因系进一步研究。;位于染色体1和10上的抽穗期QTL座位为新检测的座位。对新检测的F2不育和抽穗期QTL座位正在建立相应的近等基因系以精确定位和克隆上述基因。     

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.     

Construction of an Interspecific Genetic Map Based on InDel and SSR for Mapping the QTLs Affecting the Initiation of Flower Primordia in Pepper (Capsicum spp.)

Re-sequencing permits the mining of genome-wide variations on a large scale and provides excellent resources for the research community. To accelerate the development and application of molecular markers and identify the QTLs affecting the flowering time-related trait in pepper, a total of 1,038 pairs of InDel and 674 SSR primers from different sources were used for genetic mapping using the F₂ population (n = 154) derived from a cross between BA3 (C. annuum) and YNXML (C. frutescens). Of these, a total of 224 simple PCR-based markers, including 129 InDels and 95 SSRs, were validated and integrated into a map, which was designated as the BY map. The BY map consisted of 13 linkage groups (LGs) and spanned a total genetic distance of 1,249.77 cM with an average marker distance of 5.60 cM. Comparative analysis of the genetic and physical map based on the anchored markers showed that the BY map covered nearly the whole pepper genome. Based on the BY map, one major and five minor QTLs affecting the number of leaves on the primary axis (Nle) were detected on chromosomes P2, P7, P10 and P11 in 2012. The major QTL on P2 was confirmed based on another subset of the same F₂ population (n = 147) in 2014 with selective genotyping of markers from the BY map. With the accomplishment of pepper whole genome sequencing and annotations (release 2.0), 153 candidate genes were predicted to embed in the Nle2.2 region, of which 12 important flowering related genes were obtained. The InDel/SSR-based interspecific genetic map, QTLs and candidate genes obtained by the present study will be useful for the downstream isolation of flowering time-related gene and other genetic applications for pepper.     

Localization of a novel recessive powdery mildew resistance gene from common wheat line RD30 in the terminal region of chromosome 7AL

Segregation analysis of resistance to powdery mildew in a F₂ progeny from the cross Chinese Spring (CS) × TA2682c revealed the inheritance of a dominant and a recessive powdery mildew resistance gene. Selfing of susceptible F₂ individuals allowed the establishment of a mapping population segregating exclusively for the recessive resistance gene. The extracted resistant derivative showing full resistance to each of 11 wheat powdery mildew isolates was designated RD30. Amplified fragment length polymorphism (AFLP) analysis of bulked segregants from F₃s showing the homozygous susceptible and resistant phenotypes revealed an AFLP marker that was associated with the recessive resistance gene in repulsion phase. Following the assignment of this AFLP marker to wheat chromosome 7A by means of CS nullitetrasomics, an inspection of simple sequence repeat (SSR) loci evenly spaced along chromosome 7A showed that the recessive resistance gene maps to the distal region of chromosome 7AL. On the basis of its close linkage to the Pm1 locus, as inferred from connecting partial genetic maps of 7AL of populations CS × TA2682c and CS × Virest (Pm1e), and its unique disease response pattern, the recessive resistance gene in RD30 was considered to be novel and tentatively designated mlRD30.Communicated by C. Möllers     

Detection of quantitative trait loci for heading date based on the doubled haploid progeny of two elite Chinese wheat cultivars

Quantitative trait loci (QTLs) with epistatic and QTL × environment (QE) interaction for heading date were studied using a doubled haploid (DH) population containing 168 progeny lines derived from a cross between two elite Chinese wheat cultivars Huapei 3 × Yumai 57 (Triticum aestivum L.). A genetic map was constructed based on 305 marker loci, consisting of 283 SSR loci and 22 EST-SSR markers, which covered a total length of 2141.7 cM with an average distance of 7.02 cM between adjacent markers in the genome. QTL analyses were performed using a mixed linear model approach. Two main-effect QTLs and two pairs of digenic epistatic effects were detected for heading date on chromosomes 1B, 2B, 5D, 6D, 7A, and 7D at three different environments in 2005 and 2006 cropping seasons. A highly significant QTL with an F-value 148.96, designated as Qhd5D, was observed within the Xbarc320-Xwmc215 interval on chromosome 5DL, accounting for 53.19% of the phenotypic variance and reducing days-to-heading by 2.77 days. The Qhd5D closely links with a PCR marker Xwmc215 with the genetic distance 2.1 cM, which can be used in molecular marker-assisted selection (MAS) in wheat breeding programs. Moreover, the Qhd5D was located on the similar position of well-characterised vernalization sensitivity gene Vrn-D1. We are also spending more efforts to develop near-isogenic lines to finely map the Qhd5D and clone the gene Vrn-D1 through map-based cloning. The Qhd1B with additive effect on heading date has not been reported in previous linkage mapping studies, which might be a photoperiod-sensitive gene homoeologous to the Ppd-H2 gene on chromosome 1B. No main-effect QTLs for heading date were involved in epistatic effects.     

Accumulation of additive effects generates a strong photoperiod sensitivity in the extremely late-heading rice cultivar ‘Nona Bokra’

Many rice cultivars that originated from lower-latitude regions exhibit a strong photoperiod sensitivity (PS) and show extremely late heading under long-day conditions. Under natural day-length conditions during the cropping season in Japan, the indica rice cultivar ‘Nona Bokra’ from India showed extremely late heading (202 days to heading) compared to the japonica cultivar ‘Koshihikari’ (105 days), from Japan. To elucidate the genetic factors associated with such extremely late heading, we performed quantitative trait locus (QTL) analyses of heading date using an F₂ population and seven advanced backcross progeny (one BC₁F₂ and six BC₂F₂) derived from a cross between ‘Nona Bokra’ and ‘Koshihikari’. The analyses revealed 12 QTLs on seven chromosomes. The ‘Nona Bokra’ alleles of all QTLs contributed to an increase in heading date. Digenic interactions were rarely observed between QTLs. Based on the genetic parameters of the QTLs, such as additive effects and percentage of phenotypic variance explained, these 12 QTLs are likely generate a large proportion of the phenotypic variation observed in the heading dates between ‘Nona Bokra’ and ‘Koshihikari’. Comparison of chromosomal locations between heading date QTLs detected in this study and QTLs previously identified in ‘Nipponbare’ × ‘Kasalath’ populations revealed that eight of the heading date QTLs were recognized nearby the Hd1, Hd2, Hd3a, Hd4, Hd5, Hd6, Hd9, and Hd13. These results suggest that the strong PS in ‘Nona Bokra’ was generated mainly by the accumulation of additive effects of particular alleles at previously identified QTLs.     

QTLs for earliness and yield-forming traits in the Lubuski × CamB barley RIL population under various water regimes

Drought has become more frequent in Central Europe causing large losses in cereal yields, especially of spring crops. The development of new varieties with increased tolerance to drought is a key tool for improvement of agricultural productivity. Material for the study consisted of 100 barley recombinant inbred lines (RILs) (LCam) derived from the cross between Syrian and European parents. The RILs and parental genotypes were examined in greenhouse experiments under well-watered and water-deficit conditions. During vegetation the date of heading, yield and yield-related traits were measured. RIL population was genotyped with microsatellite and single nucleotide polymorphism markers. This population, together with two other populations, was the basis for the consensus map construction, which was used for identification of quantitative trait loci (QTLs) affecting the traits. The studied lines showed a large variability in heading date. It was noted that drought-treatment negatively affected the yield and its components, especially when applied at the flag leaf stage. In total, 60 QTLs were detected on all the barley chromosomes. The largest number of QTLs was found on chromosome 2H. The main QTL associated with heading, located on chromosome 2H (Q.HD.LC-2H), was identified at SNP marker 5880–2547, in the vicinity of Ppd-H1 gene. SNP 5880–2547 was also the closest marker to QTLs associated with plant architecture, spike morphology and grain yield. The present study showed that the earliness allele from the Syrian parent, as introduced into the genome of an European variety could result in an improvement of barley yield performance under drought conditions.     

A High-Density SNP Map of Sunflower Derived from RAD-Sequencing Facilitating Fine-Mapping of the Rust Resistance Gene R12

A high-resolution genetic map of sunflower was constructed by integrating SNP data from three F₂ mapping populations (HA 89/RHA 464, B-line/RHA 464, and CR 29/RHA 468). The consensus map spanned a total length of 1443.84 cM, and consisted of 5,019 SNP markers derived from RAD tag sequencing and 118 publicly available SSR markers distributed in 17 linkage groups, corresponding to the haploid chromosome number of sunflower. The maximum interval between markers in the consensus map is 12.37 cM and the average distance is 0.28 cM between adjacent markers. Despite a few short-distance inversions in marker order, the consensus map showed high levels of collinearity among individual maps with an average Spearman''s rank correlation coefficient of 0.972 across the genome. The order of the SSR markers on the consensus map was also in agreement with the order of the individual map and with previously published sunflower maps. Three individual and one consensus maps revealed the uneven distribution of markers across the genome. Additionally, we performed fine mapping and marker validation of the rust resistance gene R₁₂, providing closely linked SNP markers for marker-assisted selection of this gene in sunflower breeding programs. This high resolution consensus map will serve as a valuable tool to the sunflower community for studying marker-trait association of important agronomic traits, marker assisted breeding, map-based gene cloning, and comparative mapping.     

Genetic Map Construction and Quantitative Trait Locus (QTL) Detection of Six Economic Traits Using an F2 Population of the Hybrid from Saccharina longissima and Saccharina japonica

Saccharina (Laminaria) is one of the most important economic seaweeds. Previously, four genetic linkage maps of Saccharina have been constructed and five QTLs have been identified. However, they were not enough for its breeding. In this work, Saccharina longissima (♀) and Saccharina japonica (♂), which showed obvious differences in morphology and genetics, were applied in hybridization to yield the F₂ mapping population with 102 individuals. Using these 102 F₂ hybrids, the genetic linkage map of Saccharina was constructed by MapMaker software based on 37 amplified fragment length polymorphisms (AFLPs), 22 sequence-related amplified polymorphisms (SRAPs) and 139 simple sequence repeats (SSRs) markers. Meanwhile, QTL analysis was performed for six economic traits. The linkage map constructed in this research consisted of 422 marker loci (137 AFLPs, 57 SRAPs and 228 SSRs), which formed 45 linkage groups (LGs) with an average marker space of 7.92 cM; they spanned a total length of 2233.1 cM, covering the whole estimated genome size. A total of 29 QTLs were identified for six economic traits, which explained 1.06 to 64.00% of phenotypic variation, including three QTLs for frond length (FL) and raw weight (RW), five QTLs for frond width (FW), two QTLs for frond fascia width (FFW) and frond thickness (FT), and fourteen QTLs for base shape (BS). The results of this research will improve the breeding efficiency and be beneficial for marker-assisted selection (MAS) schemes in Saccharina breeding.     

Quantitative trait loci for resistance to spot blotch caused by Bipolarissorokiniana in wheat (T.aestivum L.) lines ‘Ning 8201’ and ‘Chirya 3’

Spot blotch caused by Bipolaris sorokiniana is a destructive disease of wheat in warm and humid wheat growing regions of the world. To identify quantitative trait loci (QTLs) for spot blotch resistance, two mapping populations were developed by making the crosses between common susceptible cultivar ‘Sonalika’ with the resistant breeding lines ‘Ning 8201’ and ‘Chirya 3’. Single seed descent derived F₆, F₇, F₈ lines of the first cross ‘Ning 8201’ × ‘Sonalika’ were evaluated for resistance to spot blotch in three blocks in each of the 3 years. After screening of 388 pairs of simple sequence repeat primers between the two parents, 119 polymorphic markers were used to genotype the mapping population. Four QTLs were identified on the chromosomes 2AS, 2BS, 5BL and 7DS and explained 62.9% of phenotypic variation in a simultaneous fit. The QTL on chromosome 2A was detected only in 1 year and explained 22.7% of phenotypic variation. In the second cross (‘Chirya 3’ × ‘Sonalika’), F₇ and F₈ population were evaluated in three blocks in each of the 2 years. In this population, five QTLs were identified on chromosomes 2BS, 2DS, 3BS, 7BS and 7DS. The QTLs identified in the ‘Chirya 3’ × ‘Sonalika’ population explained 43.4% of phenotypic variation in a simultaneous fit. The alleles for reduced disease severity in both the populations were derived from the respective resistant parent. The QTLs QSb.bhu-2B and QSb.bhu-7D from both populations were placed in the same deletion bins, 2BS1-0.53-0.75 and 7DS5-0.36-0.61, respectively. The closely linked markers Xgwm148 to the QTL on chromosome 2B and Xgwm111 to the QTL on chromosome 7D are potentially diagnostic markers for spot blotch resistance.     

A consensus framework map of durum wheat (Triticum durum Desf.) suitable for linkage disequilibrium analysis and genome-wide association mapping

Background

Durum wheat (Triticum durum Desf.) is a tetraploid cereal grown in the medium to low-precipitation areas of the Mediterranean Basin, North America and South-West Asia. Genomics applications in durum wheat have the potential to boost exploitation of genetic resources and to advance understanding of the genetics of important complex traits (e.g. resilience to environmental and biotic stresses). A dense and accurate consensus map specific for T. durum will greatly facilitate genetic mapping, functional genomics and marker-assisted improvement.

Results

High quality genotypic data from six core recombinant inbred line populations were used to obtain a consensus framework map of 598 simple sequence repeats (SSR) and Diversity Array Technology^® (DArT) anchor markers (common across populations). Interpolation of unique markers from 14 maps allowed us to position a total of 2,575 markers in a consensus map of 2,463 cM. The T. durum A and B genomes were covered in their near totality based on the reference SSR hexaploid wheat map. The consensus locus order compared to those of the single component maps showed good correspondence, (average Spearman’s rank correlation rho ρ value of 0.96). Differences in marker order and local recombination rate were observed between the durum and hexaploid wheat consensus maps. The consensus map was used to carry out a whole-genome search for genetic differentiation signatures and association to heading date in a panel of 183 accessions adapted to the Mediterranean areas. Linkage disequilibrium was found to decay below the r² threshold = 0.3 within 2.20 cM, on average. Strong molecular differentiations among sub-populations were mapped to 87 chromosome regions. A genome-wide association scan for heading date from 27 field trials in the Mediterranean Basin and in Mexico yielded 50 chromosome regions with evidences of association in multiple environments.

Conclusions

The consensus map presented here was used as a reference for genetic diversity and mapping analyses in T. durum, providing nearly complete genome coverage and even marker density. Markers previously mapped in hexaploid wheat constitute a strong link between the two species. The consensus map provides the basis for high-density single nucleotide polymorphic (SNP) marker implementation in durum wheat.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-873) contains supplementary material, which is available to authorized users.