A Consensus Microsatellite-Based Linkage Map for the Hermaphroditic Bay Scallop (Argopecten irradians) and Its Application in Size-Related QTL Analysis

Bay scallop (Argopecten irradians) is one of the most economically important aquaculture species in China. In this study, we constructed a consensus microsatellite-based genetic linkage map with a mapping panel containing two hybrid backcross-like families involving two subspecies of bay scallop, A. i. irradians and A. i. concentricus. One hundred sixty-one microsatellite and one phenotypic (shell color) markers were mapped to 16 linkage groups (LGs), which corresponds to the haploid chromosome number of bay scallop. The sex-specific map was 779.2 cM and 781.6 cM long in female and male, respectively, whereas the sex-averaged map spanned 849.3 cM. The average resolution of integrated map was 5.9 cM/locus and the estimated coverage was 81.3%. The proportion of distorted markers occurred more in the hybrid parents, suggesting that the segregation distortion was possibly resulted from heterospecific interaction between genomes of two subspecies of bay scallop. The overall female-to-male recombination rate was 1.13∶1 across all linked markers in common to both parents, and considerable differences in recombination also existed among different parents in both families. Four size-related traits, including shell length (SL), shell height (SH), shell width (SW) and total weight (TW) were measured for quantitative trait loci (QTL) analysis. Three significant and six suggestive QTL were detected on five LGs. Among the three significant QTL, two (qSW-10 and qTW-10, controlling SW and TW, respectively) were mapped on the same region near marker AiAD121 on LG10 and explained 20.5% and 27.7% of the phenotypic variance, while the third (qSH-7, controlling SH) was located on LG7 and accounted for 15.8% of the phenotypic variance. Six suggestive QTL were detected on four different LGs. The linkage map and size-related QTL obtained in this study may facilitate marker-assisted selection (MAS) in bay scallop.     

Genetic linkage map construction and QTL mapping of cadmium accumulation in radish (Raphanus sativus L.)

Cadmium (Cd) is a widespread soil pollutant and poses a significant threat to human health via the food chain. Large phenotypic variations in Cd concentration of radish roots and shoots have been observed. However, the genetic and molecular mechanisms of Cd accumulation in radish remain to be elucidated. In this study, a genetic linkage map was constructed using an F(2) mapping population derived from a cross between a high Cd-accumulating cultivar NAU-Dysx and a low Cd-accumulating cultivar NAU-Yh. The linkage map consisted of 523 SRAP, RAPD, SSR, ISSR, RAMP, and RGA markers and had a total length of 1,678.2 cM with a mean distance of 3.4 cM between two markers. All mapped markers distributed on nine linkage groups (LGs) having sizes between 134.7 and 236.8 cM. Four quantitative trait loci (QTLs) for root Cd accumulation were mapped on LGs 1, 4, 6, and 9, which accounted for 9.86 to 48.64 % of all phenotypic variance. Two QTLs associated with shoot Cd accumulation were detected on LG1 and 3, which accounted for 17.08 and 29.53 % of phenotypic variance, respectively. A major-effect QTL, qRCd9 (QTL for root Cd accumulation on LG9), was identified on LG 9 flanked by NAUrp011_754 and EM5me6_286 markers with a high LOD value of 23.6, which accounted for 48.64 % of the total phenotypic variance in Cd accumulation of F(2) lines. The results indicated that qRCd9 is a novel QTL responsible for controlling root Cd accumulation in radish, and the identification of specific molecular markers tightly linked to the major QTL could be further applied for marker-assisted selection (MAS) in low-Cd content radish breeding program.     

Genetic mapping of hop (Humulus lupulus L.) applied to the detection of QTLs for alpha-acid content.

The map locations and effects of quantitative trait loci (QTLs) were estimated for alpha-acid content in hop (Humulus lupulus L.) using amplified fragment length polymorphism (AFLP) and microsatellite marker (simple sequence repeat (SSR)) genetic linkage maps constructed from a double pseudotestcross. The mapping population consisted of 111 progeny from a cross between the German hop cultivar 'Magnum', which exhibits high levels of alpha-acids, and a wild Slovene male hop, 2/1. The progeny segregated quantitatively for alpha-acid content determined in 2002, 2003, and 2004. The maternal map consisted of 96 markers mapped on 14 linkage groups defining 661.90 cM of total map distance. The paternal map included 70 markers assigned to 12 linkage groups covering 445.90 cM of hop genome. QTL analysis indicated 4 putative QTLs (alpha1, alpha2, alpha3, and alpha4) on linkage groups (LGs) 03, 01, 09, and 03 of the female map, respectively. QTLs explained 11.9%-24.8% of the phenotypic variance. The most promising QTL to be used in marker-assisted selection is alpha2, the peak of which colocated exactly with the AFLP marker. Three chalcone synthase-like genes (chs2, chs3, and chs4) involved in hop bitter acid synthesis mapped together on LG04 of the female map. Saturation of the maps, particularly the putative QTL regions, will be carried out using SSR markers, and the stability of the QTLs will be tested in the coming years.     

Mapping quantitative trait loci for a common bean (Phaseolus vulgaris L.) ideotype.

Breeding a model plant that encompasses individual traits thought to enhance yield potential, known as ideotype breeding, has traditionally focused on phenotypic selection of plants with desirable morphological traits. Broadening this breeding method to the molecular level through the use of molecular markers would avoid the environmental interactions associated with phenotypic selection. A population of 110 F5 recombinant inbred lines (RILs), derived from the cross between WO3391 and 'OAC Speedvale', was used to develop a genetic linkage map consisting of 105 random amplified polymorphic DNA (RAPD), simple sequence repeat (SSR), and sequence-tagged site (STS) markers. The map has a total length of 641 cM distributed across 8 linkage groups (LGs). Five of them were aligned on the core linkage map of bean. Twenty-one quantitative trait loci (QTLs) were identified over three environments for eight agronomic and architectural traits previously defined for a bean (Phaseolus vulgaris L.) ideotype. The QTLs were mapped to seven LGs with several regions containing QTLs for multiple traits. At least one QTL was located for each trait and a maximum of four were associated with lodging. Total explained phenotypic variance ranged from 10.6% for hypocotyl diameter to 45.4% for maturity. Some of the QTLs identified will be useful for early generation selection of tall, upright, high-yielding lines in a breeding program.     

RAPD和SSR两种标记构建的中国对虾遗传连锁图谱

利用RAPD和SSR分子标记结合拟测交策略,对中国对虾(Fenneropenaeuschinensis)“黄海1号”雌虾与野生雄虾作为亲本进行单对杂交产生的F1代,采用RAPD和SSR两种分子标记技术初步构建了中国对虾雌、雄遗传连锁图谱。对460个RAPD引物和44对SSR引物进行筛选,共选出61个RAPD引物和20对SSR引物,用于对父母本和82个F1个体进行遗传分析。共得到母本分离标记146个(RAPD标记128个,微卫星标记18个)和父本分离标记127个(RAPD标记109个,微卫星标记18个)。雌性图谱包括8个连锁群、9个三联体和14个连锁对,标记间平均间隔为11·28cM,图谱共覆盖1173cM,覆盖率为59·36%;雄性图谱包括10个连锁群、12个三联体和7个连锁对,标记间平均间隔为12·05cM,图谱共覆盖1144·6cM,覆盖率为62·01%。中国对虾遗传图谱的构建为其分子标记辅助育种、比较基因组作图及数量性状位点的定位与克隆奠定了基础。     

Construction of a high-density genetic map using specific length amplified fragment markers and identification of a quantitative trait locus for anthracnose resistance in walnut (Juglans regia L.)

Background

Walnut (Juglans regia, 2n = 32, approximately 606 Mb per 1C genome) is an economically important tree crop. Resistance to anthracnose, caused by Colletotrichum gloeosporioides, is a major objective of walnut genetic improvement in China. The recently developed specific length amplified fragment sequencing (SLAF-seq) is an efficient strategy that can obtain large numbers of markers with sufficient sequence information to construct high-density genetic maps and permits detection of quantitative trait loci (QTLs) for molecular breeding.

Results

SLAF-seq generated 161.64 M paired-end reads. 153,820 SLAF markers were obtained, of which 49,174 were polymorphic. 13,635 polymorphic markers were sorted into five segregation types and 2,577 markers of them were used to construct genetic linkage maps: 2,395 of these fell into 16 linkage groups (LGs) for the female map, 448 markers for the male map, and 2,577 markers for the integrated map. Taking into account the size of all LGs, the marker coverage was 2,664.36 cM for the female map, 1,305.58 cM for the male map, and 2,457.82 cM for the integrated map. The average intervals between two adjacent mapped markers were 1.11 cM, 2.91 cM and 0.95 cM for three maps, respectively. ‘SNP_only’ markers accounted for 89.25 % of the markers on the integrated map. Mapping markers contained 5,043 single nucleotide polymorphisms (SNPs) loci, which corresponded to two SNP loci per SLAF marker. According to the integrated map, we used interval mapping (Logarithm of odds, LOD > 3.0) to detect our quantitative trait. One QTL was detected for anthracnose resistance. The interval of this QTL ranged from 165.51 cM to 176.33 cM on LG14, and ten markers in this interval that were above the threshold value were considered to be linked markers to the anthracnose resistance trait. The phenotypic variance explained by each marker ranged from 16.2 to 19.9 %, and their LOD scores varied from 3.22 to 4.04.

Conclusions

High-density genetic maps for walnut containing 16 LGs were constructed using the SLAF-seq method with an F1 population. One QTL for walnut anthracnose resistance was identified based on the map. The results will aid molecular marker-assisted breeding and walnut resistance genes identification.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1822-8) contains supplementary material, which is available to authorized users.     

Mapping quantitative trait loci (QTL) for body weight, length and condition factor traits in backcross (BC1) family of Common carp (Cyprinus carpio L.)

Body weight and length are economical important traits in aquaculture species influenced by quantitative trait loci (QTL) and environmental factors. In this study, a backcross (BC1) common carp family, with 86 progeny, was utilized to construct genetic map for preliminary QTL mapping. The genetic map was constructed with 366 markers, including 191 SNP from gene, coverage 50 linkage groups with an average marker distance of 18.5 cM. A total of fourteen QTLs associated with body weight (BW), body length (BL) and condition factor (K) were detected on ten linkage groups (LGs). Among these QTLs detected, three (qBW8, qBL8 and qK8) were associated with BW, BL and K respectively, were mapped on LG8. qBW8 and qK8 were identified on similar interval neared locus HLJ2394 explained 14.9 and 20.9 % of the phenotype variance, while qBL8 was identified on separate nearby locus HLJ571 with 30.8 % of phenotype variance. Two QTLs, qBW13 and qK13, related with BW and K separately, were found on LG13 at different locus with phenotype variance of 25.3 and 20.9 %. Other two QTLs, qBW19 and qBL19, associated to BW and BL were mapped on same region near SNP0626 on LG19, and explained 10.3 and 15.6 % of phenotype variance. While other seven QTLs related with BW and BL were located on different LGs. Confidential interval was ranged from 1.1 to 10 cM in the present study. These markers, with lower QTL interval, have great influence on the body weight and length. Therefore, these QTLs will be helpful to find out the genes related with specific trait.     

大豆遗传图谱的构建和若干农艺性状的QTL定位分析

大豆许多重要农艺性状都是由微效多基因控制的数量性状,对这些数量性状进行QTL定位是大豆数量性状遗传研究领域的一个重要内容.本研究利用栽培大豆科新3号为父本、中黄20为母本杂交得到含192个单株的F2分离群体,构建了含122 个SSR标记、覆盖1719.6cM、由33个连锁群组成的连锁遗传图谱.利用复合区间作图法,对该群体的株高、主茎节数、单株粒重和蛋白质含量等农艺性状的调查数据进行QTL分析,共找到两个株高QTL,贡献率分别为9.15%和6.08%;两个主茎节数QTL,贡献率分别为10. 1%和8.6%;一个蛋白质含量QTL,贡献率为9.8%;一个单株粒重QTL,贡献率为11.4% .通过遗传作图共找到与所定位的4个农艺性状QTL连锁的6个SSR标记,这些标记可以应用于大豆种质资源的分子标记辅助选择,从而为大豆分子标记辅助育种提供理论依据.     

Linkage analysis and identification of quantitative trait loci associated with freeze tolerance and turf quality traits in St. Augustinegrass

St. Augustinegrass [Stenotaphrum secundatum (Walt.) Kuntze] is a warm-season turfgrass commonly grown in the southern USA. In this study, the first linkage map for all nine haploid chromosomes of the species was constructed for cultivar ‘Raleigh’ and cultivar ‘Seville’ using a pseudo-F₂ mapping strategy. A total of 160 simple sequence repeat markers were mapped to nine linkage groups (LGs) covering a total distance of 1176.24 cM. To demonstrate the usefulness of the map, quantitative trait loci (QTL) were mapped controlling field winter survival, laboratory-based freeze tolerance, and turf quality traits. Multiple genomic regions associated with these traits were identified. Moreover, overlapping QTL were found for winterkill and spring green up on LG 3 (99.21 cM); turf quality, turf density, and leaf texture on LG 3 (68.57–69.50 cM); and surviving green tissue and regrowth on LGs 1 (38.31 cM), 3 (77.70 cM), 6 (49.51 cM), and 9 (34.20 cM). Additional regions, where QTL identified in both field and laboratory-based/controlled environment freeze testing co-located, provided strong support that these regions are good candidates for true gene locations. These results present the first complete linkage map produced for St. Augustinegrass, providing a template for further genetic mapping. Additionally, markers linked to the QTL identified may be useful to breeders for transferring these traits into new breeding lines and cultivars.     

Primary genome scan for complex body shape‐related traits in the common carp Cyprinus carpio

To identify quantitative trait loci (QTL) that affect body shape in common carp Cyprinus carpio, a linkage map, 2159·23 cM long, was constructed with a total of 307 markers covering 51 linkage groups (LG). The map included 167 new single nucleotide polymorphism (SNP) markers derived from expressed sequence tags (EST) together with 140 microsatellite markers reported earlier. A primary genome scan was conducted for QTL for standard length (L_S), head length (L_H), body height (H_B), body width (W_B) and tail length (L_TAIL) in an F1 line containing 92 offspring. A total of 15 suggestive QTL on six LGs were found to associate with L_S, L_H, H_B, W_B and L_TAIL which explained 10·7–17·4% of the variance. Five significant QTL were detected for body‐shape related traits and located for LGs (lg1, 12 and 20). These QTL included: one associated with L_S (21·1% variance explained), three for H_B (almost 20% variance explained) and one for W_B (20·7% variance explained).     

Construction of a genetic linkage map in <Emphasis Type="Italic">Fenneropenaeus chinensis</Emphasis> (Osbeck) using RAPD and SSR markers

The primary genetic linkage maps of Fenneropenaeus chinensis (Osbeck) were constructed by using the “two-way pseudo-testcross” strategy with RAPD and SSR markers. Parents and F1 progeny were used as segregating populations. Sixty-one RAPD primers and 20 pairs of SSR primers were screened from 460 RAPD primers and 44 pairs of SSR primers. These primers were used to analyze the parents and 82 progeny of the mapping family. About 146 primers (128 RAPDs, 18 microsatellites) in the female and 127 primers (109 RAPDs, 18 microsatellites) in the male were segregating markers. The female linkage map included eight linkage groups, nine triplets and 14 doublets, spanning 1,173 cM with the average marker density of 11.28 cM, and the observed coverage was 59.36%. The male linkage map included 10 linkage groups, 12 triplets and seven doublets, spanning 1,144.6 cM with the average marker density of 12.05 cM, and the observed coverage was 62.01%. The construction of the F. chinensis genetic linkage maps here opened a new prospect for marker-assisted selection program, comparative genomics and quantitative trait loci (QTL) gene location and cloning.     

Genetic maps of SSR and SRAP markers in diploid orchardgrass (Dactylis glomerata L.) using the pseudo-testcross strategy

Orchardgrass (Dactylis glomerata L.) is one of the most important cool-season forage grasses commonly grown throughout the temperate regions of the world. The objective of this work was to construct a diploid (2n = 2x = 14) orchardgrass genetic linkage map useful as a framework for basic genetic studies and plant breeding. A combination of simple sequence repeat (SSR) and sequence-related amplified polymorphism (SRAP) molecular markers were used for map construction. The linkage relationships among 164 SSRs and 108 SRAPs, assayed in a pseudo-testcross F1 segregating population generated from a cross between two diploid parents, were used to construct male (01996) and female (YA02-103) parental genetic maps. The paternal genetic map contains 90 markers (57 SSRs and 33 SRAPs) over 9 linkage groups (LGs), and the maternal genetic map is composed of 87 markers (54 SSRs and 33 SRAPs) assembled over 10 LGs. The total map distance of the male map is 866.7 centimorgans (cM), representing 81% genome coverage, whereas the female map spans 772.0 cM, representing 75% coverage. The mean map distance between markers is 9.6 cM in the male map and 8.9 cM in the female map. About 14% of the markers remained unassigned. The level of segregation distortion observed in this cross was 15%. Homology between the two maps was established between five LGs of the male map and five LGs of the female map using 10 bridging markers. The information presented in this study establishes a foundation for extending genetic mapping in this species, serves as a framework for mapping quantitative trait loci (QTLs), and provides basic information for future molecular breeding studies.     

Development of genetic maps of the citrus varieties ‘Murcott’ tangor and ‘Pêra’ sweet orange by using fluorescent AFLP markers

The progeny of 87 BC(1) hybrids of 'Murcott' tangor and 'Pera' sweet orange, genotyped with fluorescent amplified fragment length polymorphism (fAFLP) markers, was used for the construction of genetic maps for both citrus varieties. Mapping strategies, considering the progeny as a result of backcrossing and cross-pollination, were exploited in Mapmaker 2.0 (LOD score >or= 3.0 and or= 3.0 and theta 相似文献   

Construction of a SSR-based genetic map and identification of QTL for domestication traits using recombinant inbred lines from a cross between wild and cultivated cowpea (<Emphasis Type="Italic">V. unguiculata</Emphasis> (L.) Walp.)

Cowpea (Vigna unguiculata (L.) Walp.) is a grain legume commonly grown and consumed in many parts of the tropics and subtropics. A genetic linkage map was constructed using simple sequence repeat (SSR) markers and a recombinant inbred (RI) population of159 individuals derived from a cross between the breeding line 524B, a California Blackeye, and 219-01, a perennial wild cowpea from Kenya. Out of 912 primer combinations predicted to amplify SSRs in cowpea, 639 reliably produced amplification products in PCR assays and 202 (31.6%) were polymorphic between the two parents. These polymorphic SSRs were used to construct a genetic map consisting of 11 linkage groups (LGs) spanning 677 cM, with an average distance between markers of 3 cM. Agronomic traits related to domestication (seed weight, pod shattering) were analyzed together with the genotypic data. Six quantitative trait loci (QTL) for seed size were revealed with the phenotypic variation ranging from 8.9 to 19.1%. Four QTL for pod shattering were identified with the phenotypic variation ranging from 6.4 to 17.2%. The QTL for seed size and pod shattering mainly cluster in two areas of LGs 1 and 10, facilitating the use of marker-assisted selection to eliminate undesirable wild phenotypes in breeding activities involving introgression of traits from wild germplasm. The generation of an SSR-based molecular map and additional trait-linked markers also contributes to the expanding tool kit available to cowpea breeders, especially in Africa.     

Construction of a linkage map based on a <Emphasis Type="Italic">Lathyrus sativus</Emphasis> backcross population and preliminary investigation of QTLs associated with resistance to ascochyta blight

A linkage map of the Lathyrus sativus genome was constructed using 92 backcross individuals derived from a cross between an accession resistant (ATC 80878) to ascochyta blight caused by Mycosphaerella pinodes and a susceptible accession (ATC 80407). A total of 64 markers were mapped on the backcross population, including 47 RAPD, seven sequence-tagged microsatellite site and 13 STS/CAPS markers. The map comprised nine linkage groups, covered a map distance of 803.1 cM, and the average spacing between markers was 15.8 cM. Quantitative trait loci (QTL) associated with ascochyta blight resistance were detected using single-point analysis and simple and composite interval mapping. The backcross population was evaluated for stem resistance in temperature-controlled growth room trials. One significant QTL, QTL1, was located on linkage group 1 and explained 12% of the phenotypic variation in the backcross population. A second suggestive QTL, QTL2, was detected on linkage group 2 and accounted for 9% of the trait variation. The L. sativus R-QTL regions detected may be targeted for future intergenus transfer of the trait into accessions of the closely related species Pisum sativum.     

QTL mapping of yield, agronomic and quality traits in tetraploid potato (Solanum tuberosum subsp. tuberosum)

Interval mapping of quantitative trait loci (QTL) for 16 yield, agronomic and quality traits in potato was performed on a tetraploid full-sib family comprising 227 clones from a cross between processing clone 12601ab1 and table cultivar Stirling. Thirty-eight AFLP primer combinations and six SSRs provided 514 informative markers which formed a molecular marker map comprising 12 linkage groups (LGs) in 12601ab1 (nine with four homologous chromosomes) which were aligned with 12 in Stirling (11 with four homologous chromosomes), with four partial groups remaining in 12601ab1. Two LGs were identified unequivocally as chromosomes IV and V and eight others were tentatively assigned with chromosomes VII and X unidentified. All of the traits scored had moderately high heritabilities with 54–92% of the variation in clone means over 3 years and two replicates being due to genetic differences. A total of 39 QTLs were identified. A QTL for maturity was identified on chromosome V which explained 56% of the phenotypic variance, whereas the other QTLs individually explained between 5.4 and 16.5%. However, six QTLs were detected for after-cooking blackening and four for each of regularity of tuber shape, fry colour both after storage at 4 and 10°C and sprouting. Just two QTLs were found for each of yield, the two ‘overall’ scores, crop emergence, tuber size and common scab and just one QTL was detected for each of dry matter content, keeping quality, growth cracks and internal condition. The implications for practical potato breeding and for practical linkage and QTL analysis in autotetraploids are discussed.     

Identification of novel QTL for black tea quality traits and drought tolerance in tea plants (<Emphasis Type="Italic">Camellia sinensis</Emphasis>)

Tea (Camellia sinensis) contains polyphenols and caffeine which have been found to be of popular interest in tea quality. Tea production relies on well-distributed rainfall which influence tea quality. Phenotypic data for two segregating tea populations TRFK St 504 and TRFK St 524 were collected and used to identify the quantitative trait loci (QTL) influencing tea biochemical and drought stress traits based on a consensus genetic map constructed using the DArTseq platform. The populations comprised 261 F₁ clonal progeny. The map consisted of 15 linkage groups which corresponds to chromosome haploid number of tea plant (2n?=?2×?=?30) and spanned 1260.1 cM with a mean interval of 1.1 cM between markers. A total of 16 phenotypic traits were assessed in the two populations. Both interval and multiple QTL mapping revealed a total of 47 putative QTL in the 15 LGs associated with tea quality and percent relative water content at a significant genome-wide threshold of 5%. In total, six caffeine QTL, 25 catechins QTL, three theaflavins QTL, nine QTL for tea taster score, and three QTL for percent relative water contents were detected. Out of these 47 QTL, 19 QTL were identified for ten traits in three main regions on LG01, LG02, LG04, LG12, LG13, and LG14. The QTL associated with caffeine, individual catechins, and theaflavins were clustered mostly in LG02 and LG04 but in different regions on the map. The explained variance by each QTL in the population ranged from 5.5 to 56.6%, with an average of 9.9%. Identification of QTL that are tightly linked to markers associated with black tea quality coupled with UPLC assay may greatly accelerate development of novel tea cultivars owing to its amenability at seedling stage. In addition, validated molecular markers will contribute greatly to adoption of marker-assisted selection (MAS) for drought tolerance and tea quality improvement.     

An AFLP and RFLP linkage map and quantitative trait locus (QTL) analysis of growth traits in Salix

A genetic linkage map of Salix (2n = 38), composed of 325 AFLP and 38 RFLP markers has been constructed. The map was based on a population ( n = 87) derived from a cross between the male hybrid clone "Bj?rn" ( Salix viminalis x Salix schwerinii) and the female clone "78183" ( S. viminalis). Three hundred fifty seven AFLPs corresponding to DNA polymorphisms heterozygous in one parent and null in the other were scored. A total of 87 RFLP probes, most (83) derived from the Populus genome, yielded 39 and 11 polymorphic loci segregating in a 1:1 and 1:2:1 ratio respectively. Two maps, one for each parent, were constructed according to the "two-way pseudo-testcross" mapping strategy. The S. viminalis x S. schwerinii map (2,404 cM) included 217 markers and formed 26 major linkage groups while S. viminalis (1,844 cM) consisted of 146 markers placed on 18 major groups. In addition, eight and 14 additional minor linkage groups composed of less than four markers (doubles and triplets) were obtained in the S. viminalis x S. schwerinii and the S. viminalis maps, respectively. Both maps provided 70-80% genome coverage with an average density of markers of 14 cM. To investigate possible homologies between the parental maps, 20 AFLPs and 11 RFLPs segregating in 3:1 or 1:2:1 ratios were included in the linkage analysis. Eight linkage groups homologous between the two maps were detected. The present genetic map was used to identify quantitative trait loci (QTLs) affecting growth-related traits. Eleven QTLs were identified; seven QTLs for height growth, one QTL for stem diameter, one QTL for the height: diameter ratio, one QTL for the number of vegetative buds during flowering time and one QTL for the number of shoots. The estimated magnitude of the QTL effect ranged from 14 to 22% of the total phenotypic variance. One QTL associated with height growth and one affecting the height: diameter ratio were overlapping in the same marker interval with the QTL affecting stem diameter. QTL stability over years was estimated for traits measured in multiple years. Generally, QTLs were only significant in a single year although two QTLs for height growth were close to reaching the significance level in 2 consecutive years.     

Mapping QTL for Omega-3 Content in Hybrid Saline Tilapia

Tilapia is one of most important foodfish species. The low omega-3 to omega-6 fatty acid ratio in freshwater tilapia meat is disadvantageous for human health. Increasing omega-3 content is an important task in breeding to increase the nutritional value of tilapia. However, conventional breeding to increase omega-3 content is difficult and slow. To accelerate the increase of omega-3 through marker-assisted selection (MAS), we conducted QTL mapping for fatty acid contents and profiles in a F₂ family of saline tilapia generated by crossing red tilapia and Mozambique tilapia. The total omega-3 content in F₂ hybrid tilapia was 2.5 ± 1.0 mg/g, higher than that (2.00 mg/g) in freshwater tilapia. Genotyping by sequencing (GBS) technology was used to discover and genotype SNP markers, and microsatellites were also genotyped. We constructed a linkage map with 784 markers (151 microsatellites and 633 SNPs). The linkage map was 2076.7 cM long and consisted of 22 linkage groups. Significant and suggestive QTL for total lipid content were mapped on six linkage groups (LG3, -4, -6, -8, -13, and -15) and explained 5.8–8.3% of the phenotypic variance. QTL for omega-3 fatty acids were located on four LGs (LG11, -18, -19, and -20) and explained 5.0 to 7.5% of the phenotypic variance. Our data suggest that the total lipid and omega-3 fatty acid content were determined by multiple genes in tilapia. The markers flanking the QTL for omega-3 fatty acids can be used in MAS to accelerate the genetic improvements of these traits in salt-tolerant tilapia.     

Construction of an integrated consensus map of the apple genome based on four mapping populations

An integrated consensus genetic map for apple was constructed on the basis of segregation data from four genetically connected crosses (C1?=?Discovery × TN10-8, C2?=?Fiesta × Discovery, C3?=?Discovery × Prima, C4?=?Durello di Forli × Fiesta) with a total of 676 individuals using CarthaGene® software. First, integrated female–male maps were built for each population using common female–male simple sequence repeat markers (SSRs). Then, common SSRs over populations were used for the consensus map integration. The integrated consensus map consists of 1,046 markers, of which 159 are SSR markers, distributed over 17 linkage groups reflecting the basic chromosome number of apple. The total length of the integrated consensus map was 1,032 cM with a mean distance between adjacent loci of 1.1 cM. Markers were proportionally distributed over the 17 linkage groups (χ ²?=?16.53, df?=?16, p?=?0.41). A non-uniform marker distribution was observed within all of the linkage groups (LGs). Clustering of markers at the same position (within a 1-cM window) was observed throughout LGs and consisted predominantly of only two to three linked markers. The four integrated female–male maps showed a very good colinearity in marker order for their common markers, except for only two (CH01h01, CH05g03) and three (CH05a02z, NZ02b01, Lap-1) markers on LG17 and LG15, respectively. This integrated consensus map provides a framework for performing quantitative trait locus (QTL) detection in a multi-population design and evaluating the genetic background effect on QTL expression.