Genetic linkage map of Chinese native variety faba bean (Vicia faba L.) based on simple sequence repeat markers

Simple sequence repeat (SSR) marker is a powerful tool for construction of genetic linkage map which can be applied for quantitative trait loci (QTL) and marker‐assisted selection (MAS). In this study, a genetic map of faba bean was constructed with SSR markers using a 129 F₂ individuals population derived from the cross of Chinese native variety 91825 (large seed) and K1563 (small seed). By screening 11 551 SSR primers between two parents, 149 primer pairs were detected polymorphic and used for F₂ population analysis. This SSR‐based genetic linkage map consisted of 15 linkage groups with 128 SSR. The map encompassed 1587 cM with an average genetic distance of 12.4 cM. The genetic map generated in this study will be beneficial for genetic studies of faba bean for identification of marker‐locus‐trait associations as well as comparative mapping among faba bean, pea and grasspea.     

Genome mapping and molecular markers identification for yield,yield component and fibre quality traits in tetraploid cotton

The identification of quantitative trait loci (QTL) across different environments is a prerequisite for marker‐assisted selection (MAS) in crop improvement programmes. CottonSNP63k Illumina infinium array was used for genotyping 178 inter‐specific recombinant inbred lines and the parents, and identified 1,667 homozygous polymorphic markers between the parents. Of these, 1,430 markers were used for the construction of linkage map after removing 237 redundant markers. The genetic map spans a total genetic length of 3,149.8 cM with an average marker interval size of 2.2 cM. The phenotypic data from five environments were analysed separately using inclusive composite interval mapping which identified a total of 56 QTL explaining phenotypic variances (PVE) in the range of 8.18%–28.91%. There were 11 and 24 major QTL found for fibre quality and yield components, respectively. A total of 64 QTL were identified through Multi‐Environment Trials analysis, of which 34 recorded QTL × Environment interactions.     

Identification of new QTL for salt tolerance from rice variety Pokkali

Salt stress is an ever-present threat to rice production worldwide. Rice salinity tolerance is complex, both genetically and physiologically. The success and effectiveness in selecting salt-tolerant rice variety require the identification of QTL for the tolerance and closely linked molecular markers. In the present study, a RIL population consisting of 148 lines, derived from a cross between IR29 (salt-sensitive) and Pokkali (salt-tolerant), was used to identify new QTL for salt tolerance and investigate the relationships between salt stress caused injury and the changes in different physiological and morphological traits at the seedling stage. 14,470 high-quality SNP markers generated by the Rice 56K SNP array were converted to 1,467 bin markers for linkage mapping. A high-density genetic linkage map covering 1,680.9 cM was constructed, with the physical to genetic distance ratio being 222 Kb/cM. In total, 23 QTL for different salt tolerance indices were identified, including the previously reported Saltol which is currently used in breeding programmes. Three QTL for salt injury score (SIS) were located on chromosomes 1, 4 and 12, all being closely related to the long-distant Na⁺ transport from roots to shoots. These QTL showed additive effects, thus can be effectively used in breeding programme to pyramid various tolerance genes.     

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.     

Molecular mapping of quantitative trait loci for domestication traits and β-glucan content in a wheat recombinant inbred line population

Genetic maps are useful for analysis of quantitative trait loci (QTLs) and for marker-assisted selection (MAS) in breeding. A simple sequence repeat (SSR) marker linkage map of common wheat was constructed based on recombination inbred lines (RILs) derived from a cross between Chinese Spring and spelt wheat. The map included 264 loci on all wheat chromosomes covering 2,345.2 cM with 962, 794.6, and 588.6 cM for the A, B, and D genomes, respectively. Using the RILs and the map, we detected 42 putative QTLs on 15 chromosomes for ear length, spikelet number, spike compactness, kernel length, kernel width, kernel height and β-glucan content. Each QTL explained 4–45% of the phenotypic variation. Five QTL cluster regions were detected on chromosomes 1A, 5AL, 2B, 2D, and 4D. The first QTLs for β-glucan content in wheat were identified on chromosomes 3A, 1B, 5B, and 6D.     

QTL mapping of improving forage maize starch degradability in European elite maize germplasm

Improving maize starch content is of great importance for both forage and grain yield. In this study, 13 starch degradability traits were analysed including percentage of the seedling area, floury endosperm, hard endosperm of total grain area, percentage of the floury endosperm surface and vitreousness ratio surface hard: floury endosperm surface, etc. We mapped quantitative trait loci (QTL) in a biparental population of 309 doubled haploid lines based on field phenotyping at two locations. A genetic linkage map was constructed using 168 SSR (simple sequence repeat) markers, which covered 1508 cM of the maize genome, with an average distance of 9.0 cM. Close phenotypic and genotypic correlations were found for all traits, and were all statistically significant (p = 0.01) at two locations. Major QTL for more than two traits were detected, especially in two regions in bins 4.05–4.06 and 7.04–7.05, associated with 13 and 9 traits, respectively. This study contributes to marker‐assisted breeding and also to fine mapping candidate genes associated with maize starch degradability.     

Mapping QTL for resistance to botrytis grey mould in chickpea

Botrytis grey mould (BGM) caused by Botrytis cinerea Pers. ex. Fr. is the second most important foliar disease of chickpea (Cicer arietinum L.) after ascochyta blight. An intraspecific linkage map of chickpea consisting of 144 markers assigned on 11 linkage groups was constructed from recombinant inbred lines (RILs) of a cross that involved a moderately resistant kabuli cultivar ICCV 2 and a highly susceptible desi cultivar JG 62. The length of the map obtained was 442.8 cM with an average interval length of 3.3 cM. Three quantitative trait loci (QTL) which together accounted for 43.6% of the variation for BGM resistance were identified and mapped on two linkage groups. QTL1 explained about 12.8% of the phenotypic variation for BGM resistance and was mapped on LG 6A. It was found tightly linked to markers SA14 and TS71rts36r at a LOD score of 3.7. QTL2 and QTL3 accounted for 9.5 and 48% of the phenotypic variation for BGM resistance, respectively, and were mapped on LG 3. QTL 2 was identified at LOD 2.7 and flanked by markers TA25 and TA144, positioned at 1 cM away from marker TA25. QTL3 was a strong QTL detected at LOD 17.7 and was flanked by TA159 at 12 cM distance on one side and TA118 at 4 cM distance on the other side. This is the first report on mapping of QTL for BGM resistance in chickpea. After proper validation, these QTL will be useful in marker-assisted pyramiding of BGM resistance in chickpea.     

Identification of two major quantitative trait locus for fresh seed dormancy using the diversity arrays technology and diversity arrays technology‐seq based genetic map in Spanish‐type peanuts

Seed quality for both germination in the next generation and for human consumption is adversely affected due to preharvest sprouting in peanut. It also makes seeds more vulnerable to infection by a number of pathogens. Therefore, it is desirable to have 2–3 weeks of fresh seed dormancy (FSD) in the peanut varieties. In this context, one F₂ population was developed from a cross between non‐dormant (ICGV 00350) and dormant (ICGV 97045) genotypes. Phenotyping of this population showed control of the trait by two recessive genes. In parallel, genotyping of the population with Diversity Arrays Technology (DArT) and DArT‐seq markers provided a genetic map with 1152 loci covering a map distance of 2423.12 cM and map density of 2.96 cM/loci. Quantitative trait locus (QTL) analysis identified two major QTLs, namely qfsd‐1 and qfsd‐2 explaining 22.14% and 71.21% of phenotypic variation, respectively. These QTLs, after validation in different genetic backgrounds, may be useful for molecular breeding for FSD in peanut.     

QTL mapping of resistance in lentil (Lens culinaris ssp. culinaris) to ascochyta blight (Ascochyta lentis)

Quantitative trait locus (QTL) analysis of ascochyta blight resistance in lentil was conducted using genomic maps developed from two F₂ populations, viz. ILL5588/ILL7537 and ILL7537/ILL6002. Five QTLs for ascochyta blight resistance were identified by composite interval mapping (CIM) across four linkage groups (LG) in population ILL5588/ILL7537. Three QTLs were identified by CIM in population ILL7537/ILL6002 (two in close proximity on LGI and one on LGII). Two of these coincided with regions identified using multiple interval mapping (MIM) and were shown to be conditioned by dominant and partial dominant gene action. Together, they accounted for approximately 50% of the phenotypic variance of disease severity. Comparison between the two populations revealed a potentially common QTL and several common regions that contained markers significantly associated with resistance. This study demonstrated the transferability of QTLs among populations and identified markers closely linked to the major QTL that may be useful for future marker‐assisted selection for disease resistance.     

Mapping QTL for seed yield and canning quality following processing of black bean (<Emphasis Type="Italic">Phaseolus vulgaris</Emphasis> L.)

Quantitative trait loci (QTL) analysis was conducted to identify QTL for seed yield and color retention following processing of a recombinant inbred line (RIL) black bean population. A population of 96 RILs were derived from the cross of black bean cultivars ‘Jaguar’ and 115M and evaluated in replicated trials at one location over 4 years (2004–2007) in Michigan. A 119-point genetic map constructed using simple sequence repeat (SSR), sequence related amplified polymorphism (SRAP), target region amplified polymorphism (TRAP) and phenotypic markers spanned fifteen linkage groups (LG) or 460 cM of the bean genome. Fourteen QTL for yield and color retention in four environments were identified by composite interval mapping on six linkage groups. A major QTL SY10.2^J115 for seed yield was identified on LG B10 with additional QTL on B3, B5, and B11. Color retention following processing was associated with loci on B1, B3, B5, B8, and B11. 115M possessed positive alleles for yield, but negative alleles for color retention. Some QTL for yield and color retention co-localized with regions identified in previous studies while others, particularly for color retention, were unique. Additional QTL for agronomic and canning quality traits were detected and individual contributions to future black bean breeding are discussed.     

Molecular mapping of a major QTL conferring resistance to SCMV based on immortal RIL population in maize

Sugarcane mosaic virus (SCMV) is one of devastating pathogens in maize (Zea mays L.), and causes serious yield loss in susceptible cultivars. An effective solution to control the virus is utilizing resistant genes to improve the resistance of susceptible materials, whereas the basic work is to analyze the genetic basis of resistance. In this study, maize inbred lines Huangzao4 (resistant) and Mo17 (susceptible) were used to establish an F₉ immortal recombinant inbred line (RIL) population containing 239 RILs. Based on this segregation population, a genetic map was constructed with 100 simple sequence repeat (SSR) markers selected from 370 markers, and it covers 1421.5 cM of genetic distance on ten chromosomes, with an average interval length of 14.2 cM. Analysis of the genetic map and resistance by mapping software indicated that a major quantitative trait locus (QTL) was between bin6.00 and bin6.01 on chromosome 6, linked with marker Bnlg1600 (0.1 cM of interval). This QTL could account for 50.0% of phenotypic variation, and could decrease 27.9% of disease index.     

Co-location of seed oil content,seed hull content and seed coat color QTL in three different environments in <Emphasis Type="Italic">Brassica napus</Emphasis> L.

Increasing seed oil content is an important breeding goal for Brassica napus L. (B. napus). The identification of quantitative trait loci (QTL) for seed oil content and related traits is important for efficient selection of B. napus cultivars with high seed oil content. To get better knowledge on these traits, a molecular marker linkage map for B. napus was constructed with a recombinant inbred lines (RIL) population. The length of the map was 1,589 cM with 451 markers distributed over 25 linkage groups. QTL for seed oil content, seed hull content and seed coat color in three environments were detected by composite interval mapping (CIM) tests. Eleven QTL accounted for 5.19–13.57% of the variation for seed oil content. Twelve QTL associated with seed hull content were identified with contribution ranging from 5.80 to 22.71% and four QTL for seed coat color accounted for 5.23–15.99% of the variation. It is very interesting to found that co-localization between QTL for the three traits were found on N8. These results indicated the possibility to combine favorable alleles at different QTL to increase seed oil content, as well as to combine information about the relationship between seed oil content and other traits.     

Quantitative trait loci analysis of stem strength and related traits in soybean

Stem strength is one of the major influencing factors of lodging in soybean [Glycine max (L.) Merr.] as well as other crops. To identify quantitative trait loci (QTL) associated with stem strength and related traits in soybean, a recombinant inbred line (RIL) population consisting of 165 lines derived from Zhongdou No. 29 × Zhongdou No. 32 was used in 3 years. Significant positive correlations were found among the four traits (stem strength, stem diameter, number of nodes, root dry weight). A linkage map spanning 1,240.7 cM was constructed using 245 SSR (simple sequence repeat) markers and a phenotypic marker (leaflet shape). By composite interval mapping and two-round strategy of QTL meta-analysis, 32 consensus QTL and 19 unique QTL were identified, respectively. Of eight pleiotropic unique QTL, two QTL (uq.A2-2 and uq.A2-3) located at the intervals of 23.2–26.8 and 38.5–42.4 cM on linkage group A2, respectively, were associated with all the four traits. Additive × environment (ae) interaction effects, epistasis (aa) and epistasis × environment (aae) interaction effects of QTL were detected as well. The results provide useful information for further genetic studies on stem strength of soybean.     

Evaluation of genomic approaches for marker‐based improvement of lodging tolerance in triticale

Lodging tolerance is an important agronomic trait as it can have a severe negative impact on grain yield and quality. Here, we used a large mapping population of 647 doubled haploid triticale lines derived from four families to dissect the genetic architecture underlying lodging tolerance and to assess different approaches for a genomics‐based improvement of the trait. The plants were evaluated for lodging in two environments and genotyped with 1710 genomewide DArT markers. We observed a large genotypic variation for lodging and transgressive segregation in all families. Employing two complementary QTL mapping approaches, we identified both main effect and epistatic QTL. Using cross‐validation, we showed that the proportion of genotypic variance explained by the detected QTL is low, thus limiting the efficiency of marker‐assisted selection to improve this trait. By contrast, the cross‐validated predictive ability of genomic prediction was approximately twice as high as that of the QTL‐based selection approaches. In conclusion, our results show that lodging tolerance is a complex trait that can be improved by classical breeding but also assisted by marker‐based approaches.     

大豆重组自交系群体NJRIKY遗传图谱的加密及其应用效果

作物基因组研究,包括基因或数量性状位点(QTL)定位、图位克隆以及物理图谱构建等,首先必须建立具有丰富标记信息的高密度遗传连锁图谱。由科丰1号和南农1138-2杂交组合衍生的重组自交系群体NJRIKY已经构建了4张大豆遗传连锁图谱,但由于遗传信息和标记数目不够充分,在基因和QTL作图时仍然存在精确度和准确度问题。为增加NJRIKY图谱密度,本研究在967对SSR引物中获得了401个多态性SSR标记。结合其他分子数据,使用作图软件Mapmaker/Exp3.0b,获得一张含有553个遗传标记,25个连锁群,总长2071.6cM,平均图距3.70cM的新遗传连锁图谱,其中SSR标记316个,RFLP标记197个,EST标记39个,形态标记1个。连锁群上大于20cM的标记间隔由原来42个减少到2个。原图谱的3个SMV抗性基因定位于D1b连锁群末端的开放区间上且仅与一个RFLP标记连锁,利用加密图谱对Rsc-3、Rsc-7、Rsc-9、Rsc-13、Rsa、Rn1和Rn3等7个SMV抗性基因重定位,全部位于D1b连锁群,与相邻分子标记距离均小于6cM,其中Rsc-9、Rn1、Rsa的距离小于1cM,Rsc-13与EST标记GMKF168a共分离。对本群体农艺性状进行QTL重定位,获得8个性状相关的42个主效QTL,其中20个QTL遗传贡献率大于10%,与原图谱比较,新定位的各QTL的标记区间明显缩短,与相邻标记的连锁更加紧密。     

Localization of QTL for basal root thickness in <Emphasis Type="Italic">japonica</Emphasis> rice and effect of marker-assisted selection for a major QTL

Root traits are key components of plant adaptation to drought environment. By using a 120 recombined inbred lines (RILs) rice population derived from a cross between IRAT109, a japonica upland rice cultivar and Yuefu, a japonica lowland rice cultivar, a complete genetic linkage map with 201 molecular markers covering 1,833.8 cM was constructed and quantitative trait loci (QTLs) associated with basal root thickness (BRT) were identified. A major QTL, conferring thicker BRT, located on chromosome 4, designated brt4, explained phenotypic variance of 20.6%, was selected as target QTL to study the effects of marker-assisted selection (MAS) using two early segregating populations derived from crosses between IRAT109 and two lowland rice cultivars. The results showed that the flanking markers of brt4 were genetically stable in populations with different genetic backgrounds. In the two populations under upland conditions, the difference between the means of BRT of plants carrying positive and negative favorable alleles at brt4 flanking markers loci was significant. Phenotypic effects of BRT QTL brt4 were 5.05–8.16%. When selected plants for two generations were planted at Beijing and Hainan locations under upland conditions, MAS effects for BRT QTL brt4 were 4.56–18.56% and 15.46–26.52% respectively. The means of BRT for the homozygous plants were greater than that of heterozygous plants. This major QTL might be useful for rice drought tolerance breeding. L. Liu and P. Mu are contributed equally to this work.     

苦荞SSR分子遗传图谱的构建及分析

构建苦荞遗传连锁图谱,为今后有关苦荞基因组结构、重要农艺性状QTL定位、分子标记辅助育种和基因克隆等研究工作奠定基础。以栽培苦荞‘滇宁一号’和苦荞野生近缘种杂交产生的119份F4代分离材料为作图群体,利用SSR分子标记来构建苦荞的分子遗传连锁图谱。本研究构建的连锁图谱包含15个连锁群,由89个标记组成,其中偏分离的标记有22个,占24.7%,每条连锁群上的标记在2~16之间。连锁群长度在6.9~165.8 cM的范围,覆盖基因组860.2 cM,总平均长度9.7 cM。本研究构建了首张苦荞SSR遗传连锁图谱,为苦荞QTL定位、基因克隆、遗传选育等研究奠定了基础。     

Evaluation of newly developed SSR markers and identification of quantitative trait loci for bast fibre cellulose in white jute (Corchorus capsularis)

Cellulose is one of the main chemical component of bast fibre in jute. However, quantitative trait loci (QTL) for bast fibre cellulose content remains elusive. In this study, we identified 846 new SSR markers from 70,792 unigenes in the NCBI and validated them in a panel of 24 diverse jute accessions. Of 846 SSRs, 748 (88.41%) were successfully amplified, and 585 (69.14%) showed polymorphisms, implying that these are high‐quality SSRs. Furthermore, 585 SSRs along with 5,074 polymorphic SLAF (specific locus amplified fragment) and 173 InDel markers were used to reconstruct a high‐dense linkage map in a recombinant inbred population with 104 F₈ lines. Totally, 835 markers were successfully mapped to a whole length of 604.5 cM with a mean distance of 2.84 cM between adjacent markers. Furthermore, five QTLs for bast fibre cellulose were identified. One major QTL (qBFC1‐1) was stable in 2 years and explained average phenotypic variance with 14.34%. These results may be useful for developing enhanced bast fibre quality in white jute through marker‐assisted selection (MAS) breeding.     

Construction of an integrated genetic map based on maternal and paternal lineages of tea (Camellia sinensis)

Genetic study on important traits of tea is difficult because of its self-incompatibility in nature. Moreover, development of a new variety usually needs more than 20 years, since it takes many years from seedling to matured plants for trait investigation. Genetic map is an essential tool for genetic study and breeding. In this study, we have developed an integrated genetic map of tea (Camellia sinensis) using a segregating F1 population derived from a cross between two commercial cultivars (‘TTES 19’ and ‘TTES 8’). A total of 574 polymorphic markers (including SSR, CAPS, STS, AFLP, ISSR and RAPD), 69 markers with highly significant levels of segregation distortion (P < 0.001) (12.0 %) were excluded from further analyses. Of the 505 mapped markers, there were 265 paternal markers (52.5 %), 163 maternal markers (32.3 %), 65 doubly heterozygous dominant markers (12.9 %), and 12 co-dominant markers (2.4 %). The co-dominant markers and doubly heterozygous dominant markers were used as bridge loci for the integration of the paternal and maternal maps. The integrated map comprised 367 linked markers, including 36 SSR, 3 CAPS, 1 STS, 250 AFLP, 13 ISSR and 64 RAPD that were assigned to 18 linkage groups. The linkage groups represented a total map length of 4482.9 cM with a map density of 12.2 cM. This genetic map has the highest genetic coverage so far, which could be applied to comparative mapping, QTL mapping and marker assisted selection in the future.     

甘蓝型油菜遗传图谱的构建及芥酸含量的QTL分析

一个由甘蓝型油菜品种Quantum (黄花、低芥酸)和人工合成的甘蓝型油菜品系No.2127-17（白花、高芥酸）为亲本材料建立的DH群体中芥酸呈现单基因的遗传模式。为了发展与芥酸紧密连锁的分子标记对其实行有效的控制,随机选择121个结实正常的DH系为作图群体,利用SSR和RAPD标记构建了一张甘蓝型油菜的遗传连锁图谱。在亲本间检测