QTL analysis of quality traits in the spring wheat cross RL4452 × 'AC Domain'

Wheat grain quality is a complex group of traits of tremendous importance to wheat producers, end‐users and breeders. Quantitative trait locus (QTL) analysis studied the genetics of milling, mixograph, farinograph, baking, starch and noodle colour traits in the spring wheat population RL4452/‘AC Domain’. Forty‐seven traits were measured on the population and 99 QTLs were detected over 18 chromosomes for 41 quality traits. Forty‐four of these QTLs mapped to three major QTL clusters on chromosomes 1B, 4D, and 7D. Fourteen QTLs mapped near Glu‐B1, 20 QTLs mapped near a major plant height QTL on chromosome 4D, and 10 QTLs mapped near a major time to maturity QTL on chromosome 7D. Large QTLs were detected for grain and flour protein content, farinograph absorption, mixograph parameters, and dietary fibre on chromosome 2BS. QTLs for yellow alkaline noodle colour parameter L* mapped to chromosomes 5B and 5D, while the largest QTL for the b* parameter mapped to 7AL.     

QTL analysis of Cercospora leaf spot resistance in sugar beet

The inheritance of Cercospora leaf spot resistance in sugar beet was investigated by means of quantitative trait loci (QTL) analysis of a segregating population of 193 individuals, using 110 AFLP and 35 restriction fragment length polymorphism (RFLP) markers. Five QTL were found through composite interval mapping on linkage groups 1, 2, 3, and 9, respectively, two of which were linked on linkage group 3. The significance of these QTL was tested by permutation analysis The QTL had mostly additive, but also certain negative dominance effects; all the resistance alleles came from the Cercospora-resistant parent. Each quantitative trait locus accounted for 7-18% of the phenotypic variation, leaving 37% of the variation unexplained. The results are discussed in relation to the potential use of marker-assisted breeding for Cercospora leaf spot resistance in sugar beet.     

Molecular mapping of QTLs for non-parasitic leaf spot resistance and comparison of half-sib DH populations in spring barley

Quantitative trait loci (QTLs) for resistance against non-parasitic leaf spots (NPLS) were first characterized in a spring barley double haploid population derived from the cross IPZ 24727/Barke (Behn et al., 2004). The aim of the present study was to identify QTLs for NPLS resistance in the half-sibling DH population IPZ 24727/Krona and to compare them with the QTLs of the population IPZ 24727/Barke. An anther culture-derived doubled haploid population of 536 DH lines was developed from the cross IPZ 24727 (resistant)/Krona (susceptible). Field trials were performed over two years in two replications, scoring NPLS and agronomic traits that might interact with NPLS. A molecular linkage map of 1035 cM was constructed based on AFLPs, SSRs and the mlo marker. QTL analyses for NPLS identified three QTLs that accounted for 30% of the phenotypic variation. For comparison of the QTLs from each DH population, a consensus map was generated comprising 277 markers with a length of 1199 cM. In both populations, the QTLs for NPLS mapped to chromosomes 1H, 4H and 7H. A common QTL with a great effect in both populations and over all environments was localized at the mlo locus on chromosome 4H, indicating that the mlo powdery mildew resistance locus has a considerable effect on NPLS susceptibility. The steps necessary to validate the QTLs and to improve the NPLS resistance by breeding were discussed.     

Identification of QTL for stalk sugar-related traits in a population of recombinant inbred lines of maize

Increasing sugar content in silage maize stalk improves its forage quality and palatability. The genetic mapping and characterization of quantitative trait loci (QTLs) is considered a valuable tool for trait enhancement, yet little information on QTL for stalk sugar content in maize has been reported. To this end, we investigated QTLs associated with stalk sugar traits including Brix, plant height (PHT), three ear leaves area (TELA), and days to silking (DTS) in two environments using a population of 202 recombinant inbred lines from a cross between YXD053, which has a high stalk sugar content, and Y6-1, which has a low stalk sugar content. A genetic map with 180 SSR and 10 AFLP markers was constructed, which spanned 1,648.6 cM of the maize genome with an average marker distance of 8.68 cM, and QTLs were detected using composite interval mapping. Seven QTLs controlling Brix were mapped on chromosomes 1, 2, 6 and 9 in the combined environments. These QTLs could explain 2.69–13.08 % of the phenotypic variance. One major QTL for Brix on chromosome 2 located between the markers bnlg1909 and umc1635 explained 13.08 % of the phenotypic variance. Y6-1 also contributed QTL allele for increased Brix on chromosome 6. One major QTLs controlling PHT on chromosome 1 and TELA on chromosome 4 were also identified and accounted for 13.68 and 12.49 % of the phenotypic variance, respectively. QTL alleles for increased DTS were located on chromosomes 1 and 5 of YXD053. Significant epistatic effects were identified in four traits, but no significant QTL × environment interactions were observed. The information presented here may be valuable for stalk sugar content improvement via marker-assisted selection in silage maize breeding programs.     

Barley—Pyrenophora graminea interaction: QTL analysis and gene mapping

Pyrenophora graminea is a seed-borne pathogen and is the causal agent of the barley leaf stripe disease. Our aim is to study the genetic basis of barley resistance to leaf stripe. A qualitatively acting resistance factor has been identified in the cultivar ‘Vada’ and the partial resistance of the cultivar ‘Proctor’ to a P. graminea isolate has been demonstrated to be dominated by a major quantitative trait locus (QTL), mapped on barley chromosome 1. Map colinearity between the leaf stripe ‘Proctor’ resistance QTLs,‘Vada’ resistance to leaf stripe, and other disease resistance loci have been investigated in this work using molecular markers. Moreover, since inoculation of barley rootlets by the fungus had been shown to induce the accumulation of several PR (pathogen-related) mRNA families, seven barley PR genes have been mapped as RFLPs, and one assigned to a chromosome arm via ditelosomic analysis to verify possible map associations with resistance QTLs. This work discusses the genetic relationships between the known leaf stripe resistance loci, resistance loci towards other seed-borne pathogens and defence gene loci.     

Fine mapping of major QTLs for alkaline tolerance at the seedling stage in maize (<Emphasis Type="Italic">Zea mays</Emphasis> L.) through genetic linkage analysis combined with high-throughput DNA sequencing

Exploiting genes and quantitative trait loci (QTLs) related to maize (Zea mays L.) alkaline tolerance is helpful for improving alkaline resistance. To explore the inheritance of maize alkaline tolerance at the seedling stage, a mapping population comprising 151 F_2:3 lines derived from the maize cross between Zheng58, tolerant to alkaline, and Chang7-2, sensitive to alkaline, was used to establish a genetic linkage map with 200 SSR loci across the 10 maize linkage groups, with an average interval of 6.5 cM between adjacent markers. QTLs for alkaline resistant traits of alkaline tolerance rating (ATR), germination rate (GR), relative conductivity (RC), weight per plant (WPP) and proline content (PC) were detected. The obtained results were as follows: Five QTLs on chromosomes 2, 5 and 6 (GR and WPP: chr. 2; PC and ATR: chr. 5; and RC: chr. 6) were mapped. For precise mapping of the QTLs related to alkaline resistance, two bulked deoxyribonucleic acid (DNA) pools were constructed using individual DNAs from the most tolerant 30 F₂ individuals and the most sensitive 30 F₂ individuals according to the ATR and used to establish a high density map of SLAF markers strongly associated with the ATR by specific locus amplified fragment sequencing (SLAF-Seq) combined with super bulked segregant analysis (superBSA). One marker-intensive region involved three SLAFs at 296,000–6,203,000 bp on chromosome 5 that were closely related to the ATR. Combined with preliminary QTL mapping with superBSA, two major QTLs on chromosome 5 associated with alkaline tolerance at the maize seedling stage were mapped to marker intervals of dCap-SLAF31521 and dCap-SLAF31535 and phi024 and dCap-SLAF31521, respectively. These QTL regions involved 9 and 75 annotated genes, respectively. These results will be helpful for improving maize alkaline tolerance at the seedling stage by marker-assisted selection programs and will be useful for fine mapping QTLs for maize breeding.     

基于QTL定位分析小麦株高的杂种优势

为探讨小麦株高杂种优势的分子遗传基础,以小麦品种花培3号和豫麦57杂交F1经染色体加倍获得的DH群体168个株系为材料,构建了一套含168个杂交组合的"永久F2"群体。利用复合区间作图法,在3个环境中进行了基于QTL定位的株高杂种优势分析,共检测到3个加性效应位点、2个显性效应位点、4对上位效应位点(包括加性×加性、加性×显性、显性×加性和显性×显性)和20个杂种优势位点。位于2D、4D和5B2染色体上的QPh2D、QPh4D和QPh5B2在3个环境中同时被检验到,受环境影响小,表达稳定。在2D染色体上相近的区域定位出多个杂种优势位点,其中QPh2D-2和QPh2D-7可解释杂种优势表型变异的29.77%和55.77%。在7D染色体的Xwmc273.2-Xcfd175之间定位出同一个杂种优势位点Qph7D-2。结果表明,在2D、4D和7D染色体上这些区域存在一些对小麦株高的杂种优势起重要作用的位点。     

Mapping of rhizoctonia root rot resistance genes in sugar beet using pathogen response‐related sequences as molecular markers

Rhizoctonia root and crown rot caused by the fungus Rhizoctonia solani is a serious disease of sugar beet. An F_2:3 population from a cross between a resistant and a susceptible parent has been tested for R. solani resistance and a genetic map has been constructed from the corresponding F₂ parents. The map encompasses 38 expressed sequence tags (ESTs) with high similarity to genes which are involved in resistance reactions of plants (R‐ESTs) and 25 bacterial artificial chromosomes (BACs) containing nucleotide binding site (NBS)‐motifs typical for disease resistance genes. Three quantitative trait loci (QTL) for R. solani resistance were found on chromosomes 4, 5 and 7 collectively explaining 71% of the total phenotypic variation. A number of R‐ESTs were mapped in close distance to the R. solani resistance QTL. In contrast, the NBS‐BACs mapped to chromosomes 1, 3, 7 and 9 with two major clusters of NBS‐BACs on chromosome 3. No linkage between NBS‐BACs and R. solani resistance QTL was found. The data are discussed with regard to using R‐ESTs and NBS markers for mapping quantitative disease resistances.     

转基因抗虫棉产量相关性状QTL的分子标记及定位

 采用亚洲棉渐渗的纤维强度突出的陆地棉优质新品系0-153与陆地棉转基因抗虫新品系sGK9708为亲本,构建了F₂及F_2∶3分离群体。利用3869对SSR引物筛选亲本,得到125对多态性引物。进一步对183个F₂群体单株分析得到150个多态性标记位点,其中100个标记位点连锁,构建20个连锁群,共覆盖660 cM,占棉花总基因组的14.67%,每个连锁群平均包含5个标记位点,标记间平均相距6.6 cM,其中13个连锁群确定了对应的染色体。利用F₂和F_2:3数据,通过复合区间作图,共检测到28个产量及相关因素的QTLs。这些控制产量性状的QTLs只存在于5个连锁群上,成簇分布。与皮棉产量性状有关的2个QTLs,均与其它多个产量相关性状的QTLs在同一个连锁区段内,增效基因遗传效应方向一致,有必要研究其在标记辅助选择中的效果。本研究没有检测到在多世代表现稳定的QTL。因此,需要培育重组自交系,进一步明确产量性状有关QTL的遗传效应。     

QTL for rice grain quality based on a DH population derived from parents with similar apparent amylose content

A doubled haploid (DH)population consisting of 135 lines, derived from an indica (IR64) and a japonica (Azucena) rice with a similar apparent amylose content (AAC), was used to investigate the genetic factors affecting cooking and eating quality of rice. AAC,gelatinization temperature (GT), gel consistency (GC) and six starch pasting viscosity parameters were measured for quantitative trait loci (QTL) analysis using 193 molecular markers mapped on the DH population. A total of 17 QTLs were detected for the 9 traits, with at least one QTL and as many as 3 QTLs for each individual trait. No QTL for the measured parameters was found at the wx locus,possibly because of the similar AAC between the parents. Several QTLs with important effects on the variations in the measured parameters were detected in the present study which have not been found in earlier reports based on populations derived from parents with different AAC and wxgene alleles. Two interesting loci could be deduced from the present study according to the marker order compared with other genetic linkage maps. A QTL flanked by Amy2A and RG433 on the end of the long arm of chromosome 6, identified for GT, set back and consistency viscosity, might cover the gene encoding starch branching enzyme I. Similarly, a QTL flanked by RG139 and RZ58on chromosome 2, detected for hot paste viscosity and breakdown viscosity, might cover the gene encoding starch branching enzyme III. Generally, traits significantly correlated with each other shared identical QTL, but it was not true in some cases. The fine molecular mechanisms underlying these traits await further elucidation for the improvement of eating and cooking quality of rice. This revised version was published online in August 2006 with corrections to the Cover Date.     

QTL for delayed bolting after winter detected in leaf beet (Beta vulgaris L.)

Growing sugar beet (Beta vulgaris L. ssp. vulgaris) as a winter crop in cool temperate climates is expected to increase yield potential. However, this requires bolting resistance after winter. One strategy to achieve complete bolting resistance is to accumulate genes for bolting delay from various genetic resources within the B. vulgaris gene pool. To identify such genes, a QTL mapping was performed in a segregating population derived from a biennial leaf beet with delayed bolting after winter. The population was tested for bolting delay after winter in two different experiments with natural or artificial vernalization. Three QTL for bolting delay were mapped on linkage groups 3, 5 and 9 affecting bolting time by up to 19 days. These QTL could be combined with recently reported bolting QTL to develop a winter sugar beet with complete bolting resistance.     

A major QTL effect controlling resistance to powdery mildew in winter wheat at the adult plant stage

Powdery mildew is one of the major diseases of wheat in regions with a maritime or semi‐continental climate which can strongly affect grain yield. The objective of the study was to identify and compare quantitative resistance to powdery mildew of line RE9001 at the adult plant and vernalized seedling stages. RE9001 has no known Pm gene and shows a high level of adult plant resistance in the field. Using 104 recombinant inbred lines (RILs) of an RE9001 × ‘Courtot’ F8 population, a genetic map was developed with 363 markers distributed over 26 linkage groups and covering 3825 cM. The global map density was 1 locus/10.3 cM. RILs were assessed under field and tunnel greenhouse conditions for 2 years in two locations. Eleven quantitative trait loci (QTL) were detected at the adult stage and they explained 63% of the variation, depending on the environment. Three QTLs were found, at least, in the two environments. One QTL from RE9001, mapped on chromosome 2B, was stable in each environment. This QTL, QPm.inra.2B, explained 10.3–36.6% of the variation and could be mapped in the vicinity of the Pm6 gene. At the vernalized seedling stage, one QTL detected by the isolate 93‐27 could be an allele of the Pm3g gene present in ‘Courtot’. No residual effect of the Pm3g gene was detected at either stage. Markers flanking the QTL 2B could be useful tools to combine resistance to powdery mildew in wheat cultivars.     

Mapping genes for deep-seeding tolerance in barley

Deep-seeding tolerance, the emergence of seedlings from deep seeded conditions, is involved in stand establishment in semi-arid regions, where the soil surface is too dry for seed germination. Genes determining deep-seeding tolerance in barley were mapped using two doubled haploid populations derived from the following crosses: Harrington × TR306 (H/T)and Step toe × Morex (S/M). Significant quantitative trait loci (QTLs) for deep-seeding tolerance were found in each population. Two QTL sex plained 40% of the phenotypic variation in the H/T population and one QTL (S/M) 8% of the total phenotypic variance. Multiple QTLs accounting for coleoptile length and first internode length were detected in both populations. In the H/T population, there were coincident QTLs for deep-seeding tolerance, coleoptile length and first internode length on the long arm of chromosome 5H. These QTLs correspond with previously reported QTLs for abscisic acid and gibberellic acid response. QTL coincidence may be due to the pleiotropic effects of alleles at a single locus. This information may be useful for breeding programs manipulating morphological and physiological traits in order to develop varieties for semi-arid regions. This revised version was published online in August 2006 with corrections to the Cover Date.     

东乡野生稻抗褐飞虱QTL分析

野生稻是水稻抗褐飞虱基因的重要种质资源。应用东乡野生稻与栽培稻协青早B构建的2套材料,开展水稻抗褐飞虱基因鉴定研究。先以协青早B//协青早B/东乡野生稻BC₁F₅群体为材料,应用褐飞虱田间种群进行抗虫鉴定,检测到2个抗褐飞虱QTL,其中,qBph2位于水稻第2染色体RM29–RG157区间,东乡野生稻等位基因可降低死苗率22.2%;qBph7位于第7染色体RM11–RM234区间,东乡野生稻等位基因可降低死苗率43.7%。进一步以协青早B为轮回亲本,构建了BC₃F₃群体,应用褐飞虱生物型I、II和III进行抗虫鉴定,QTL分析表明qBph2抗褐飞虱生物型I和II,qBph7抗褐飞虱生物型I和III。这2个QTL对培育抗褐飞虱水稻品种具有重要应用价值。     

Mapping of QTLs associated with cadmium tolerance and accumulation during seedling stage in rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.)

Cadmium (Cd) is a non-essential element and toxic to plants. To investigate the genetics of Cd tolerance and accumulation in rice, quantitative trait loci (QTL) associated with Cd tolerance and accumulation at the seedling stage were mapped using a doubled haploid (DH) population derived from a cross between a japonica JX17 and an indica ZYQ8. A total of 22 QTLs were found to be associated with shoot height (SH), root length (RL), shoot dry weight (SDW), root dry weight (RDW), total dry weight (TDW) and chlorophyll content (CC), and 10 and 12 QTLs were identified under the control and Cd stress conditions, respectively. For Cd tolerant coefficient (CTC), 6 QTLs were detected on chromosomes 1, 3, 5, 8 and 10. Under Cd stress, 3 QTLs controlling root and shoot Cd concentrations were mapped on chromosome 6 and 7. One QTL for shoot/root rate of Cd concentration was identified on chromosome 3. The results indicated that Cd tolerance and accumulation were quantitatively inherited, and the detected QTLs may be useful for marker-assistant selection (MAS) and identification of the genes controlling Cd tolerance and accumulation in rice.     

YM型小麦温敏雄性不育系不育基因的QTL定位

YM型小麦温敏雄性不育系的不育基因被定位在1Bs染色体片段上, 但已发现的相邻分子标记与该基因的遗传距离较大, 达10 cM以上。为寻找与该基因连锁更紧密的分子标记, 以YM型温敏雄性不育系ATM3314与恢复系中国春杂交的F₂代200株为作图群体, 从1Bs的22个SSR引物中筛选出5个在亲本和F₂代中分离的SSR引物, 构建了1个包含5个标记的1Bs局部遗传连锁图谱。结合F₂代个体的育性调查, 采用复合区间作图法在YM型温敏雄性不育系的1Bs染色体上检测到不育基因的1个主效QTLrfv1-1和1个微效QTLrfv1-2。rfv1-1位于SSR标记Xgwm18和Xwmc406之间, 与两标记的遗传距离分别为6.0 cM和4.6 cM, LOD值为8.80, 加性效应23.87, 显性效应10.44, 可解释表型变异的23.91%; rfv1-2位于Xwmc406和Xbarc8之间, 与两标记的遗传距离分别为4.0 cM和3.4 cM, LOD值为3.10, 加性效应17.59, 显性效应5.99, 可解释表型变异的7.78%。本研究初步定位了YM型小麦温敏雄性不育系1Bs染色体片段上不育基因的QTL, 为进一步准确定位该基因奠定了基础。     

Dynamic analyses of rice blast resistance for the assessment of genetic and environmental effects

A doubled haploid population was employed to characterize the dynamic changes of the genetic components involved in rice blast resistance, including main-effect quantitative trait loci (QTLs), epistatic QTLs and QTL-by-environment interactions. The study was carried out at three different developmental stages of rice, using natural infection tests over 2 years. The number of main-effect QTLs, epistatic QTLs and their environmental interactions differed across the various measuring stages. One QTL ( d12 ) on chromosome 12 was detected at all stages, whereas most QTLs were active only at one or two stages in the population. These findings suggest that the unstable expression of most QTLs identified for blast resistance was influenced by the developmental status of the plants, epistatic effects between different loci and the environments in which they were grown. These findings demonstrate the complexity of expression of rice blast resistance and have important implications for durable resistance-breeding and map-based cloning of quantitative traits.     

Identification of population-specific QTLs for flowering in soybean

Flowering is an important stage in plant development and crucial for adaptation of plant species to different environments. Two soybean mapping populations were used to identify quantitative trait loci (QTLs) for days to flowering (DF) and days to maturity (DM) by genotyping simple sequence repeat (SSR) markers. Single-factor analysis of variance detected association of phenotypic data with SSR markers in each population. DF QTLs were identified on four chromosomes (chrs.); two QTLs located on chrs. 2 and 13 with Satt041 and Satt206 in the Jinpumkong 2 × SS2-2 population and other two DF QTLs were detected on chrs. 6 and 19 with Satt100 and Satt373 in the Iksannamulkong × SS2-2 population. The major QTLs associated with Satt100 explained 30.3% of maximum phenotypic variation. Especially, all DF QTLs included QTLs for DM, except Satt206 on chr. 13. Moreover, two additional DM QTLs were mapped on chrs. 10 and 11 with Satt243 and Satt359, respectively. DF QTL on chr. 2 with Satt041 was the newly identified QTL only in the Jinpumkong 2 × SS2-2 population and explained 10.3% of the phenotypic variation. The single locus of Satt100 on chr. 6 and Satt373 on chr. 19 were located on soybean genomic regions of the known flowering gene loci E1 and E3, respectively. These population-specific QTLs (Satt100 and Satt373) are the major QTLs for flowering time, putatively, they may be related to maturity QTLs with large effect. Additionally, these QTLs are valuable for marker-assisted approaches and could be widely adopted by soybean breeders.     

利用DH群体动态检测水稻抗褐飞虱数量性状基因位点

利用籼粳交珍汕97／武育粳2号F1花培获得的190个双单倍体群体(doubled—haploid population,DH系)及其构建的179个SSR分子标记遗传图谱,通过对DH系群体苗期重复接虫试验和2个不同时期对褐飞虱危害程度进行动态调查,并应用Mapmaker／exp Version3．0和Windows QTL Cartographer V2．0对水稻抗褐飞虱数量性状基因位点(quantative trait locus,QTL)进行动态检测和遗传效应分析。结果表明,在苗期对褐飞虱抗性的检测中,共检测到6个抗性QTL,分别位于第2、3、4、8和10染色体上,各QTL的LOD值分别为2．22-4．64,贡献率为5．04％～13．73％,第3染色体和第4染色体上各有1个OTL的加性效应为正值,表明来自于亲本武育粳2号的这2个位点的等位基因可以提高水稻对褐飞虱的抗性,其余4个QTL的加性效应均为负值,表明来自于亲本珍汕97的这些位点的等位基因可以提高水稻对褐飞虱的抗性。     

Mapping and validation of QTLs for resistance to an Indian isolate of Ascochyta blight pathogen in chickpea

Ascochyta blight (AB) caused by Ascochyta rabiei, is globally the most important foliar disease that limits the productivity of chickpea (Cicer arietinum L.). An intraspecific linkage map of cultivated chickpea was constructed using an F₂ population derived from a cross between an AB susceptible parent ICC 4991 (Pb 7) and an AB resistant parent ICCV 04516. The resultant map consisted of 82 simple sequence repeat (SSR) markers and 2 expressed sequence tag (EST) markers covering 10 linkage groups, spanning a distance of 724.4 cM with an average marker density of 1 marker per 8.6 cM. Three quantitative trait loci (QTLs) were identified that contributed to resistance to an Indian isolate of AB, based on the seedling and adult plant reaction. QTL1 was mapped to LG3 linked to marker TR58 and explained 18.6% of the phenotypic variance (R ²) for AB resistance at the adult plant stage. QTL2 and QTL3 were both mapped to LG4 close to four SSR markers and accounted for 7.7% and 9.3%, respectively, of the total phenotypic variance for AB resistance at seedling stage. The SSR markers which flanked the AB QTLs were validated in a half-sib population derived from the same resistant parent ICCV 04516. Markers TA146 and TR20, linked to QTL2 were shown to be significantly associated with AB resistance at the seedling stage in this half-sib population. The markers linked to these QTLs can be utilized in marker-assisted breeding for AB resistance in chickpea.