SSR-based genetic linkage map construction in pistachio using an interspecific F<Subscript>1</Subscript> population and QTL analysis for leaf and shoot traits

Pistachio is one of the most commercially important nut trees in the world. To characterize the genetic controls of horticultural traits and facilitate marker-assisted breeding in pistachio, we constructed an SSR-based linkage map using an interspecific F₁ population derived from a cross between the cultivar “Siirt” (Pistacia vera L.) and the monoecious Pa-18 genotype of Pistacia atlantica Desf. This population was also used for the first QTL analysis in pistachio on leaf and shoot characters. In total, 1312 SSR primers were screened, and 388 loci were successfully integrated into parental linkage maps. The Siirt maternal map contained 306 markers, while the “Pa-18” paternal map included 285 markers along the 15 linkage groups. The Siirt map spanned 1410.4 cM, with an average marker distance of 4.6 cM; the Pa-18 map covered 1362.5 cM with an average marker distance of 4.8 cM. Phenotypic data were collected during the growing seasons of 2015 and 2016 for four traits: leaf length (LL), leaf width (LW), leaf length/leaf width ratio (LWR), number of leaflet pairs (NLL), and young shoot color (YSC). A total of 17 QTLs were identified in the parental maps. Four QTLs for LL and LW were located on LG2 and LG4, while four QTLs for LWR ratio on LG13 and LG14, two QTLs for NLL and two QTLs for YSC were on LG7 and LG9, respectively, with similar positions in both parental maps. The SSR markers, linkage maps, and QTLs reported here will provide a valuable resource for future molecular and genetic studies in pistachio.     

Mapping Genetic Loci for Quantitative Traits of Golden Shell Color,Mineral Element Contents,and Growth-Related Traits in Pacific Oyster (<Emphasis Type="Italic">Crassostrea gigas</Emphasis>)

Golden shell color and mineral content are important economic traits of Pacific oyster (Crassostrea gigas). In this study, we mapped a series of quantitative trait loci (QTLs) that control zinc (Zn) and magnesium (Mg) content, shell color and growth performance to two sex-averaged linkage maps from the FAM-A and FAM-B families. In total, ten QTLs were identified in seven linkage groups (LGs) in the FAM-B family, and seven QTLs were identified in four linkage groups in the FAM-A family. Two QTLs affecting the trait of golden shell color were identified in LG8 of the FAM-A and LG10 of the FAM-B families, which could explain 20.2 and 10.5% of the phenotypic variations, respectively. Two QTLs for Zn content were identified that could contribute to 17.9 and 34.44% of the phenotypic variations in FAM-A. Six QTLs for Zn and Mg contents were identified in four LGs (LG1, LG2, LG5, and LG9) in FAM-B, which explained 13.5–26.7% of the phenotypic variations. In addition, seven QTLs related to oyster growth were recognized in both FAM-A and FAM-B families accounting for 14.6–36.7% of the phenotypic variations. All of the DNA markers in QTL regions were blasted and 14 genes associated with above traits were identified. The mRNA expression of these genes was determined by quantitative RT-PCR. These QTLs and candidate genes could be used as potential targets for marker-assisted selection in C. gigas breeding.     

Identification of Novel Strain-Specific and Environment-Dependent Minor QTLs Linked to Fire Blight Resistance in Apples

Since its first report almost 200 years ago, fire blight, caused by the gram-negative bacterium Erwinia amylovora, has threatened apple and pear production globally. Identifying novel genes and their functional alleles is a prerequisite to developing apple cultivars with enhanced fire blight resistance. Here, we report 13 strain-specific and environment-dependent minor QTLs linked to fire blight resistance from a segregating Malus sieversii × Malus × domestica mapping population. Interval mapping at 95% confidence and Kruskal–Wallis analysis at P value =?0.005 were used to identify QTLs for three strains of E. amylovora differing in virulence and pathogenicity. The QTLs identified explain a small to moderate part of resistance variability, and a majority was not common between years or E. amylovora strains. These QTLs are distributed in eight linkage groups of apples and comparison of their map position to previously identified fire blight resistance QTLs indicates that most are novel loci. Interaction between experimental conditions in the greenhouse and field, and between years, and differences in virulence levels of strains might be responsible for strain- and year-specific QTLs. The QTLs identified on LG10 for strain Ea273 in 2011 and strain LP101 in 2011, and on LG15 for strain LP101 could be the same QTLs identified previously with strain CFBP1430 in cultivar “Florina” and “Co-op16 × Co-op17” mapping population, respectively. We discuss the potential impact of newly identified minor fire blight QTLs and major gene-based resistance on the rate of mutation in pathogen populations to overcome resistance and durability of resistance.     

Construction of the First High-Density Genetic Linkage Map and Analysis of Quantitative Trait Loci for Growth-Related Traits in <Emphasis Type="Italic">Sinonovacula constricta</Emphasis>

The razor clam (Sinonovacula constricta) is an important aquaculture species, for which a high-density genetic linkage map would play an important role in marker-assisted selection (MAS). In this study, we constructed a high-density genetic map and detected quantitative trait loci (QTLs) for Sinonovacula constricta with an F₁ cross population by using the specific locus amplified fragment sequencing (SLAF-seq) method. A total of 315,553 SLAF markers out of 467.71 Mreads were developed. The final linkage map was composed of 7516 SLAFs (156.60-fold in the parents and 20.80-fold in each F₁ population on average). The total distance of the linkage map was 2383.85 cM, covering 19 linkage groups with an average inter-marker distance of 0.32 cM. The proportion of gaps less than 5.0 cM was on average 96.90%. A total of 16 suggestive QTLs for five growth-related traits (five QTLs for shell height, six QTLs for shell length, three QTLs for shell width, one QTL for total body weight, and one QTL for soft body weight) were identified. These QTLs were distributed on five linkage groups, and the regions showed overlapping on LG9 and LG13. In conclusion, the high-density genetic map and QTLs for S. constricta provide a valuable genetic resource and a basis for MAS.     

Construction of a sequence-based bin map and mapping of QTLs for downy mildew resistance at four developmental stages in Chinese cabbage (<Emphasis Type="Italic">Brassica rapa</Emphasis> L. ssp. <Emphasis Type="Italic">pekinensis</Emphasis>)

Specific-locus amplified fragment sequencing is a high-resolution method for genetic mapping, genotyping, and single nucleotide polymorphism (SNP) marker discovery. Previously, a major QTL for downy mildew resistance, BraDM, was mapped to linkage group A08 in a doubled-haploid population derived from Chinese cabbage lines 91–112 and T12–19. The aim of the present study was to improve the linkage map and identify the genetic factors involved in downy mildew resistance. We detected 53,692 high quality SLAFs, of which 7230 were polymorphic, and 3482 of the polymorphic markers were used in genetic map construction. The final map included 1064 bins on ten linkage groups and was 858.98 cM in length, with an average inter-locus distance of 0.81 cM. We identified six QTLs that are involved in downy mildew resistance. The four major QTLs, sBrDM8, yBrDM8, rBrDM8, and hBrDM8, for resistance at the seedling, young plant, rosette, and heading stages were mapped to A08, and are identical to BraDM. The two minor resistance QTLs, rBrDM6 (A06) and hBrDM4 (A04), were active at the rosette and heading stages. The major QTL sBrDM8 defined a physical interval of ~228 Kb on A08, and a serine/threonine kinase family gene, Bra016457, was identified as the possible candidate gene. We report here the first high-density bin map for Chinese cabbage, which will facilitate mapping QTLs for economically important traits and SNP marker development. Our results also expand knowledge of downy mildew resistance in Chinese cabbage and provide three SNP markers (A08-709, A08-028, and A08-018) that we showed to be effective when used in MAS to breed for downy mildew resistance in B. rapa.     

QTL Mapping of Wood FT-IR Chemotypes Shows Promise for Improving Biofuel Potential in Short Rotation Coppice Willow (<Emphasis Type="Italic">Salix</Emphasis> spp.)

An increasing interest to convert lignocellulosic biomass into biofuels has highlighted the potential of using willows for this purpose, due to its fast growth in short rotation coppice systems. Here, we use a mapping population of 463 individuals of a cross between Salix viminalis and S. viminalis × S. schwerinii to investigate the genetic background of different wood chemical traits, information of importance for breeding towards different uses of wood. Furthermore, using a subset of the mapping population, the correlation between biogas production and chemical traits was investigated. The phenotyping of wood was carried by Furrier-transformed-Infrared spectrometry (FT-IR) and water content analysis. Quantitative trait loci (QTLs) analysis was used to identify regions in the genome of importance for the phenotypic variation of these chemical traits. We found 27 QTLs for various traits. On linkage group (LG) VI-1, QTLs for signals assigned to G-lignin, lignin, and the S/G ratio were collocated and on LG XIV we found a cluster of QTLs representing signals assigned to lignin, cellulose, hemicellulose, and water. The QTLs explained from 3.4 to 6.9% of the phenotypic variation indicating a quantitative genetic background where many genes influence the traits. For the biogas production, a positive and negative correlation was seen with the signals assigned to acetyl and lignin, respectively. This study represents a first step in the understanding of the genetic background of wood chemical traits for willows, information needed for complementary studies, mapping of important genes, and for breeding of varieties for biofuel production purposes.     

Genetic mapping of local adaptation along the altitudinal gradient in <Emphasis Type="Italic">Abies sachalinensis</Emphasis>

Understanding the genetic bases of local adaptation in dominant conifer species is critical in predicting the impacts of rapid climate change on forest ecosystems. However, the genetic basis of adaptation is not yet fully understood due to the huge and complex genomes of conifers and the unavailability to date of suitable crossing material. In this study, we constructed a linkage map for Abies sachalinensis (2n = 24) and investigated quantitative trait loci (QTLs) associated with local adaptation along an altitudinal gradient. A segregating population of 239 seedlings was produced from a cross between two F₁ hybrids (high-altitude × low-altitude genotypes). QTL mapping of phenological and growth traits was performed using a pseudo-testcross strategy with linkage maps based on 1251 single-nucleotide polymorphism (SNP) and three simple sequence repeat (SSR) markers. Two maps consisting of 12 linkage groups with an average marker interval of ca. 3 cM were constructed for each parent. The total lengths of the maps were 1861 and 1949 cM. A permutation test identified four significant QTLs and 11 additional suggestive QTLs, with high logarithm of odds (LOD) scores (> 3.0). This is the first highly saturated linkage map produced for Abies taxa. Our results suggest that spring bud phenology is controlled by several QTLs with moderate effects. The use of the mapping population created by crossing two hybrids (high × low altitude genotypes) and numerous SNP markers enabled us to investigate the genetic basis of adaptive traits in conifer species.     

Identification and validation of quantitative trait loci controlling seed isoflavone content across multiple environments and backgrounds in soybean

Soybean is important throughout the world not only due to the high seed protein and oil but also owing to the seed isoflavone. To improve the isoflavone concentration in seeds, detecting and mining the stable and reliable quantitative trait loci (QTLs) and related genes in multiple environments and genetic backgrounds become more and more important. In view of this, a F_6:7 recombinant inbred line (RIL) population of 345 lines derived from a cross between Zheng 92116 and Liaodou14 (ZL) was genotyped using 1739 polymorphic SNP and 127 SSR markers in this study and was phenotyped for individual and total seed isoflavone in four environments over 2 years. In total, 48 additive QTLs, which explained 3.00–29.83% of seed isoflavone variation, were identified. Of them, eight QTLs (qDA1_1, qGA1_1, qTIA1_1, qDA1_2, qGA1_2, qTIA1_2, qDA1_3, qTIA1_3) with phenotypic variation explained (PVE) ranging from 14.09 to 28.59% for daidzin, genistin, and total isoflavone were located on the same region of linkage group (LG) A1. These QTLs were further verified in another RIL population derived from Zheng 92116 × Qihuang 30 (ZQ). Meanwhile, the other four overlapping QTLs on linkage group B1, which were associated with glycitin content (qGLB1_1, qGLB1_2, qGLB1_3, qGLB1_4) and explained 16.52 to 29.83% of phenotypic variation, were also verified using the ZQ population. Moreover, the individuals with different genotypes at the common flanking SNP markers for these QTLs on LGs A1 and B1 in the two mapping populations showed significant different isoflavone content, which further validate the QTL mapping results. And also, some candidate genes might participate in the isoflavone biosynthesis processes were found in these stable QTL regions. Thus, the novel and stable QTLs identified and verified in this study could be applied in marker-assisted selection breeding or map-based candidate genes cloning in soybean seed isoflavone genetic improvement in future.     

High-density SNP linkage map construction and QTL mapping for flavonoid-related traits in a tea plant (<Emphasis Type="Italic">Camellia sinensis</Emphasis>) using 2b-RAD sequencing

Background

Flavonoids are important components that confer upon tea plants a unique flavour and health functions. However, the traditional breeding method for selecting a cultivar with a high or unique flavonoid content is time consuming and labour intensive. High-density genetic map construction associated with quantitative trait locus (QTL) mapping provides an effective way to facilitate trait improvement in plant breeding. In this study, an F1 population (LJ43×BHZ) was genotyped using 2b-restriction site-associated DNA (2b-RAD) sequencing to obtain massive single nucleotide polymorphism (SNP) markers to construct a high-density genetic map for a tea plant. Furthermore, QTLs related to flavonoids were identified using our new genetic map.

Results

A total of 13,446 polymorphic SNP markers were developed using 2b-RAD sequencing, and 4,463 of these markers were available for constructing the genetic linkage map. A 1,678.52-cM high-density map at an average interval of 0.40 cM with 4,217 markers, including 427 frameset simple sequence repeats (SSRs) and 3,800 novel SNPs, mapped into 15 linkage groups was successfully constructed. After QTL analysis, a total of 27 QTLs related to flavonoids or caffeine content (CAF) were mapped to 8 different linkage groups, LG01, LG03, LG06, LG08, LG10, LG11, LG12, and LG13, with an LOD from 3.14 to 39.54, constituting 7.5% to 42.8% of the phenotypic variation.

Conclusions

To our knowledge, the highest density genetic map ever reported was constructed since the largest mapping population of tea plants was adopted in present study. Moreover, novel QTLs related to flavonoids and CAF were identified based on the new high-density genetic map. In addition, two markers were located in candidate genes that may be involved in flavonoid metabolism. The present study provides valuable information for gene discovery, marker-assisted selection breeding and map-based cloning for functional genes that are related to flavonoid content in tea plants.

     

Quantitative trait locus (QTL) analysis of fruit-quality traits for mandarin breeding in Japan

The improvement of fruit quality is an important objective in citrus breeding. Using an F₁ segregating population from a cross between citrus cultivars ‘Harehime’ (‘E647’—‘Kiyomi’ [Citrus unshiu Marcow. ‘Miyagawa Wase’ × Citrus sinensis (L.) Osbeck ‘Trovita’] × ‘Osceola’—a cultivar of clementine [Citrus clementina hort. ex Tanaka] × ‘Orland’ [Citrus paradisi Macfad. ‘Duncan’ × Citrus tangerina hort. ex Tanaka] × ‘Miyagawa Wase’) and ‘Yoshida’ ponkan (Citrus reticulata Blanco ‘Yoshida’), a SNP-based genetic linkage map was constructed and quantitative trait locus (QTL) mapping of four fruit-quality traits (fruit weight, sugar content, peel puffing, and water rot) was performed. The constructed genetic linkage map of ‘Harehime’ consisted of 442 single nucleotide polymorphisms (SNPs) on 9 linkage groups (LGs) and covered 635.8 cM of the genome, while that of ‘Yoshida’ ponkan consisted of 332 SNPs on 9 LGs and covered 892.9 cM of its genome. We identified four QTLs associated with fruit weight, one QTL associated with sugar content, three QTLs associated with peel puffing, and one QTL associated with water rot. For these QTL regions, we estimated the haplotypes of the crossed parents and verified the founding cultivars that these QTLs were originated from and their inheritance in descendant cultivars using pedigree information. QTLs identified in this study provide useful information for marker-assisted breeding of citrus in Japan.     

Construction of a high-density SNP genetic map in flue-cured tobacco based on SLAF-seq

Tobacco (Nicotiana tabacum L., 2n = 48) is an important agronomic crop and model plant. Flue-cured tobacco is the most important type and accounts for approximately 80 % of tobacco production worldwide. The low genetic diversity of flue-cured tobacco impedes the construction of a high-density genetic linkage map using simple sequence repeat (SSR) markers and warrants the exploitation of single nucleotide polymorphic (SNP) markers from genomic regions. In this article, initially using specific locus-amplified fragment sequencing, we discovered 10,891 SNPs that were subsequently used as molecular markers for genetic map construction. Combined with SSR markers, a final high-density genetic map was generated containing 4215 SNPs and 194 SSRs distributed on 24 linkage groups (LGs). The genetic map was 2662.43 cM in length, with an average distance of 0.60 cM between adjacent markers. Furthermore, by mapping the SNP markers to the ancestral genomes of Nicotiana tomentosiformis and Nicotiana sylvestris, a large number of genome rearrangements were identified as occurring after the polyploidization event. Finally, using this novel integrated map and mapping population, two major quantitative trait loci (QTLs) were identified for flue-curing and mapped to the LG6 of tobacco. This is the first report of SNP markers and a SNP-based linkage map being developed in tobacco. The high-density genetic map and QTLs related to tobacco curing will support gene/QTL fine mapping, genome sequence assembly and molecular breeding in tobacco.     

Quantitative trait locus mapping under irrigated and drought treatments based on a novel genetic linkage map in mungbean (<Emphasis Type="Italic">Vigna radiata</Emphasis> L.)

Key message

A novel genetic linkage map was constructed using SSR markers and stable QTLs were identified for six drought tolerance related-traits using single-environment analysis under irrigation and drought treatments.

Abstract

Mungbean (Vigna radiata L.) is one of the most important leguminous food crops. However, mungbean production is seriously constrained by drought. Isolation of drought-responsive genetic elements and marker-assisted selection breeding will benefit from the detection of quantitative trait locus (QTLs) for traits related to drought tolerance. In this study, we developed a full-coverage genetic linkage map based on simple sequence repeat (SSR) markers using a recombinant inbred line (RIL) population derived from an intra-specific cross between two drought-resistant varieties. This novel map was anchored with 313 markers. The total map length was 1010.18 cM across 11 linkage groups, covering the entire genome of mungbean with a saturation of one marker every 3.23 cM. We subsequently detected 58 QTLs for plant height (PH), maximum leaf area (MLA), biomass (BM), relative water content, days to first flowering, and seed yield (Yield) and 5 for the drought tolerance index of 3 traits in irrigated and drought environments at 2 locations. Thirty-eight of these QTLs were consistently detected two or more times at similar linkage positions. Notably, qPH5A and qMLA2A were consistently identified in marker intervals from GMES5773 to MUS128 in LG05 and from Mchr11-34 to the HAAS_VR_1812 region in LG02 in four environments, contributing 6.40–20.06% and 6.97–7.94% of the observed phenotypic variation, respectively. None of these QTLs shared loci with previously identified drought-related loci from mungbean. The results of these analyses might facilitate the isolation of drought-related genes and help to clarify the mechanism of drought tolerance in mungbean.

     

QTL mapping for resistance to Ceratocystis wilt in <Emphasis Type="Italic">Eucalyptus</Emphasis>

Ceratocystis wilt caused by the fungus Ceratocystis fimbriata, is currently one of the major diseases in commercial plantations of Eucalyptus trees in Brazil. Deployment of resistant genotypes has been the main strategy for effective disease management. The present study aimed at identifying genomic regions underlying the genetic control of resistance to Ceratocystis wilt in Eucalyptus by quantitative trait loci (QTL) mapping in an outbred hybrid progeny derived from a cross between (Eucalyptus dunnii × Eucalyptus grandis) × (Eucalyptus urophylla × Eucalyptus globulus). A segregating population of 127 individuals was phenotyped for resistance to Ceratocystis wilt using controlled inoculation under a completely randomized design with five clonal replicates per individual plant. The phenotypic resistance response followed a continuous variation, enabling us to analyze the trait in a quantitative manner. The population was genotyped with 114 microsatellite markers and 110 were mapped with an average interval of 12.3 cM. Using a sib-pair interval-mapping approach five QTLs were identified for disease resistance, located on linkage groups 1, 3, 5, 8, and 10, and their estimated individual heritability ranged from 0.096 to 0.342. The QTL on linkage group 3 overlaps with other fungal disease-resistance QTLs mapped earlier and is consistent with the annotation of several disease-resistance genes on this chromosome in the E. grandis genome. This is the first study to identify and attempt to quantify the effects of QTLs associated with resistance to Ceratocystis wilt in Eucalyptus.     

Mapping quantitative trait loci controlling oil content,oleic acid and linoleic acid content in sunflower (<Emphasis Type="Italic">Helianthus annuus</Emphasis> L.)

Sunflower oil with high oleic acid content is in great demand due to its nutritional as well as industrial benefits. The trait is mainly controlled by dominant alleles at a major gene, Ol, with other modifiers. The objectives of this research were to map the oil content, oleic acid and linoleic acid content in sunflower seeds. An F2 mapping population from cytoplasmic male-sterile line COSF 7A (33–35 % oleic acid) and high oleic acid inbred line HO 5–13 (88–90 % oleic acid) was developed and phenotyped for oil content, oleic acid and linoleic acid content at the F2 seed level. High phenotypic and genotypic coefficients of variation were recorded for oleic acid and linoleic acid content. High heritability and high genetic advance as percent of mean was recorded for oleic acid and linoleic acid content. This indicated the presence of the additive type of gene action controlling the traits oleic acid content and linoleic acid content. The Ol gene was mapped to linkage group (LG) 14 and tightly linked to the marker HO_Fsp_b. In addition, two more quantitative trait loci (QTLs) for oleic acid content were identified in LG8 and LG9. Two QTLs for oil content and two QTLs for linoleic acid content were also identified. All these QTLs explained over 10 % of phenotypic variation. A study was conducted with 13 genotypes differing in oil quality as well as quantity over three seasons to assess the reliability of the identified QTLs over seasons. It resulted in the identification of two potential QTLs for oleic acid as well as linoleic acid content with the markers ORS 762 and HO_Fsp_b. These markers explained more than 57.6–66.6 % of phenotypic variation. Hence it can be concluded that these markers/QTLs would be useful in the marker-assisted selection breeding programme to improve oil quality. The present study also indicated the presence of at least two other genomic regions controlling oleic and linoleic acid content in sunflower.     

Constructing a new integrated genetic linkage map and mapping quantitative trait loci for vegetative mycelium growth rate in Lentinula edodes

The most saturated linkage map for Lentinula edodes to date was constructed based on a monokaryotic population of 146 single spore isolates (SSIs) using sequence-related amplified polymorphism (SRAP), target region amplification polymorphism (TRAP), insertion–deletion (InDel) markers, and the mating-type loci. Five hundred and twenty-four markers were located on 13 linkage groups (LGs). The map spanned a total length of 1006.1 cM, with an average marker spacing of 2.0 cM. Quantitative trait loci (QTLs) mapping was utilized to uncover the loci regulating and controlling the vegetative mycelium growth rate on various synthetic media, and complex medium for commercial cultivation of L. edodes. Two and 13 putative QTLs, identified respectively in the monokaryotic population and two testcross dikaryotic populations, were mapped on seven different LGs. Several vegetative mycelium growth rate-related QTLs uncovered here were clustered on LG4 (Qmgr1, Qdgr1, Qdgr2 and Qdgr9) and LG6 (Qdgr3, Qdgr4 and Qdgr5), implying the presence of main genomic areas responsible for growth rate regulation and control. The QTL hotspot region on LG4 was found to be in close proximity to the region containing the mating-type A (MAT-A) locus. Moreover, Qdgr2 on LG4 was detected on different media, contributing 8.07 %–23.71 % of the phenotypic variation. The present study provides essential information for QTL mapping and marker-assisted selection (MAS) in L. edodes.     

基于F2群体的香菇遗传图谱构建及其在QTL定位中的应用

以171个F2双核体菌株为作图群体,通过相互配对的2个单核体的基因型推断双核体基因型,构建了第一张基于双核体群体的香菇遗传图谱。该图谱包含分布于15个连锁群的459个标记,覆盖长度为989.7cM,平均标记间隔为2.2cM。此外,以此双核体群体作为表型分离群体,定位了6个与香菇双核体菌丝生长速度相关的QTLs,位于5个连锁群上。采用全同胞单核体随机交配策略,易于构建相对大的双核体群体,用于连锁图构建和QTL定位。研究表明,在食用菌连锁图谱构建及QTL定位研究中,利用F2群体,可能为提高遗传作图效率,解决作图群体与表型分离群体间不一致问题提供新的途径。     

Construction of a genome-anchored,high-density genetic map for melon (<Emphasis Type="Italic">Cucumis melo</Emphasis> L.) and identification of <Emphasis Type="Italic">Fusarium oxysporum</Emphasis> f. sp. <Emphasis Type="Italic">melonis</Emphasis> race 1 resistance QTL

Key message

Four QTLs and an epistatic interaction were associated with disease severity in response to inoculation with Fusarium oxysporum f. sp. melonis race 1 in a recombinant inbred line population of melon.

Abstract

The USDA Cucumis melo inbred line, MR-1, harbors a wealth of alleles associated with resistance to several major diseases of melon, including powdery mildew, downy mildew, Alternaria leaf blight, and Fusarium wilt. MR-1 was crossed to an Israeli cultivar, Ananas Yok’neam, which is susceptible to all of these diseases, to generate a recombinant inbred line (RIL) population of 172 lines. In this study, the RIL population was genotyped to construct an ultra-dense genetic linkage map with 5663 binned SNPs anchored to the C. melo genome and exhibits the overall high quality of the assembly. The utility of the densely genotyped population was demonstrated through QTL mapping of a well-studied trait, resistance to Fusarium wilt caused by Fusarium oxysporum f. sp. melonis (Fom) race 1. A major QTL co-located with the previously validated resistance gene Fom-2. In addition, three minor QTLs and an epistatic interaction contributing to Fom race 1 resistance were identified. The MR-1 × AY RIL population provides a valuable resource for future QTL mapping studies and marker-assisted selection of disease resistance in melon.

     

Development of F1 hybrid population and the high-density linkage map for European aspen (<Emphasis Type="Italic">Populus tremula</Emphasis> L.) using RADseq technology

Background

Restriction-site associated DNA sequencing (RADseq) technology was recently employed to identify a large number of single nucleotide polymorphisms (SNP) for linkage mapping of a North American and Eastern Asian Populus species. However, there is also the need for high-density genetic linkage maps for the European aspen (P. tremula) as a tool for further mapping of quantitative trait loci (QTLs) and marker-assisted selection of the Populus species native to Europe.

Results

We established a hybrid F1 population from the cross of two aspen parental genotypes diverged in their phenological and morphological traits. We performed RADseq of 122 F1 progenies and two parents yielding 15,732 high-quality SNPs that were successfully identified using the reference genome of P. trichocarpa. 2055 SNPs were employed for the construction of maternal and paternal linkage maps. The maternal linkage map was assembled with 1000 SNPs, containing 19 linkage groups and spanning 3054.9 cM of the genome, with an average distance of 3.05 cM between adjacent markers. The paternal map consisted of 1055 SNPs and the same number of linkage groups with a total length of 3090.56 cM and average interval distance of 2.93 cM. The linkage maps were employed for QTL mapping of one-year-old seedlings height variation. The most significant QTL (LOD = 5.73) was localized to LG5 (96.94 cM) of the male linkage map, explaining 18% of the phenotypic variation.

Conclusions

The set of 15,732 SNPs polymorphic in aspen and high-density genetic linkage maps constructed for the P. tremula intra-specific cross will provide a valuable source for QTL mapping and identification of candidate genes facilitating marker-assisted selection in European aspen.

     

Identification of Sex-determining Loci in Pacific White Shrimp <Emphasis Type="Italic">Litopeneaus vannamei</Emphasis> Using Linkage and Association Analysis

The Pacific white shrimp Litopenaeus vannamei is a predominant aquaculture shrimp species in the world. Like other animals, the L. vannamei exhibited sexual dimorphism in growth trait. Mapping of the sex-determining locus will be very helpful to clarify the sex determination system and further benefit the shrimp aquaculture industry towards the production of mono-sex stocks. Based on the data used for high-density linkage map construction, linkage-mapping analysis was conducted. The sex determination region was mapped in linkage group (LG) 18. A large region from 0 to 21.205 cM in LG18 showed significant association with sex. However, none of the markers in this region showed complete association with sex in the other populations. So an association analysis was designed using the female parent, pool of female progenies, male parent, and pool of male progenies. Markers were de novo developed and those showing significant differences between female and male pools were identified. Among them, three sex-associated markers including one fully associated marker were identified. Integration of linkage and association analysis showed that the sex determination region was fine-mapped in a small region along LG18. The identified sex-associated marker can be used for the sex detection of this species at genetic level. The fine-mapped sex-determining region will contribute to the mapping of sex-determining gene and help to clarify sex determination system for L. vannamei.