Identification of QTLs Associated with Oil Content in a High-Oil Brassica napus Cultivar and Construction of a High-Density Consensus Map for QTLs Comparison in B. napus

Increasing seed oil content is one of the most important goals in breeding of rapeseed (B. napus L.). To dissect the genetic basis of oil content in B. napus, a large and new double haploid (DH) population containing 348 lines was obtained from a cross between ‘KenC-8’ and ‘N53-2’, two varieties with >10% difference in seed oil content, and this population was named the KN DH population. A genetic linkage map consisting of 403 markers was constructed, which covered a total length of 1783.9 cM with an average marker interval of 4.4 cM. The KN DH population was phenotyped in eight natural environments and subjected to quantitative trait loci (QTL) analysis for oil content. A total of 63 identified QTLs explaining 2.64–17.88% of the phenotypic variation were identified, and these QTLs were further integrated into 24 consensus QTLs located on 11 chromosomes using meta-analysis. A high-density consensus map with 1335 marker loci was constructed by combining the KN DH map with seven other published maps based on the common markers. Of the 24 consensus QTLs in the KN DH population, 14 were new QTLs including five new QTLs in A genome and nine in C genome. The analysis revealed that a larger population with significant differences in oil content gave a higher power detecting new QTLs for oil content, and the construction of the consensus map provided a new clue for comparing the QTLs detected in different populations. These findings enriched our knowledge of QTLs for oil content and should be a potential in marker-assisted breeding of B. napus.     

Linkage map construction using InDel and SSR markers and QTL analysis of heading traits in Brassica oleracea var. capitata L.

Cabbage heading traits are important quantitative traits that greatly affect both quality and yield of cabbage. However, the genetic control of these traits remains unclear. To detect quantitative trait loci (QTLs) associated with heading traits, a double haploid (DH) population with 196 lines was created from a cabbage hybrid 01–20 × 96–100. A genetic map with insertion–deletion and simple sequence repeat markers was constructed based on the DH population, with a total length of 934.06 cM and average interval length of 2.3 cM between adjacent markers. Field experiments in three seasons were carried out to evaluate the heading traits, including head mature period (Hm), head weight (Hw), core length (Cl), head vertical diameter (Hvd), and the ratio of Cl to Hvd (Cl/Hvd). Using the map and the trait data, 13 reliable QTLs in total were identified and 5 were found in more than one season based on the adjusted means of three seasons. Major QTLs were identified for Hm (R ² = 40.4, LOD = 14.84), Hw (R ² = 28.6, LOD = 9.83), Cl (R ² = 38.8, LOD = 15.73), Hvd (R ² = 19.2, LOD = 9.26), and Cl/Hvd (R ² = 38.8, LOD = 12.75). The most significant QTLs were Hm3.1, Cl3.1, and Cl/Hvd3.1, which were detected in three seasons with the maximum contribution rate of almost 40 %. Six active regions that harbored more than one QTL were identified on five chromosomes, and one of them contained major QTLs associated with five traits. The QTLs obtained in this study should be useful for marker-assisted selection in cabbage breeding and for understanding the genetic control of these traits.     

Linkage Map Construction and Quantitative Trait Loci Analysis for Bolting Based on a Double Haploid Population of Brassica rapa

Early bolting of Chinese cabbage （Brassica rapa L.） during spring cultivation often has detrimental effects on the yield and quality of the harvested products. Breeding late bolting varieties is a major objective of Chinese cabbage breeding programs. In order to analyze the genetic basis of bolting traits, a genetic map of B. rapa was constructed based on amplified fragment-length poiymorphism （AFLP）, sequence-related amplified poiymorphism （SRAP）, simple sequence repeat （SSR）, random amplification of polymorphic DNA （RAPD）, and isozyme markers. Marker analysis was carried out on 81 double haploid （DH） lines obtained by microspore culture from F1 progeny of two homozygous parents： B. rapa L. ssp. pekinensis （BY） （an extra-early bolting Chinese cabbage line） and B. rapa L. ssp. rapifera （MM） （an extra-late bolting European turnip line）. A total of 326 markers including 130 AFLPs, 123 SRAPs, 16 SSRs, 43 RAPDs and 14 isozymes were used to construct a linkage map with 10 linkage groups covering 882 cM with an average distance of 2.71 cM between loci. The bolting trait of each DH line was evaluated by the bolting index under controlled conditions. Quantitative trait loci （QTL） analysis was conducted using multiple QTL model mapping with MapQTL5.0 software. Eight QTLs controlling bolting resistance were identified. These QTLs, accounting for 14.1% to 25.2% of the phenotypic variation with positive additive effects, were distributed into three linkage groups. These results provide useful information for molecular marker-assisted selection of late bolting traits in Chinese cabbage breeding programs.     

QTL Mapping of Leafy Heads by Genome Resequencing in the RIL Population of Brassica rapa

Leaf heads of cabbage (Brassica oleracea), Chinese cabbage (B. rapa), and lettuce (Lactuca sativa) are important vegetables that supply mineral nutrients, crude fiber and vitamins in the human diet. Head size, head shape, head weight, and heading time contribute to yield and quality. In an attempt to investigate genetic basis of leafy head in Chinese cabbage (B. rapa), we took advantage of recent technical advances of genome resequencing to perform quantitative trait locus (QTL) mapping using 150 recombinant inbred lines (RILs) derived from the cross between heading and non-heading Chinese cabbage. The resequenced genomes of the parents uncovered more than 1 million SNPs. Genotyping of RILs using the high-quality SNPs assisted by Hidden Markov Model (HMM) generated a recombination map. The raw genetic map revealed some physical assembly error and missing fragments in the reference genome that reduced the quality of SNP genotyping. By deletion of the genetic markers in which recombination rates higher than 20%, we have obtained a high-quality genetic map with 2209 markers and detected 18 QTLs for 6 head traits, from which 3 candidate genes were selected. These QTLs provide the foundation for study of genetic basis of leafy heads and the other complex traits.     

High-Density Genetic Linkage Map Construction and QTL Mapping of Grain Shape and Size in the Wheat Population Yanda1817 × Beinong6

High-density genetic linkage maps are necessary for precisely mapping quantitative trait loci (QTLs) controlling grain shape and size in wheat. By applying the Infinium iSelect 9K SNP assay, we have constructed a high-density genetic linkage map with 269 F ₈ recombinant inbred lines (RILs) developed between a Chinese cornerstone wheat breeding parental line Yanda1817 and a high-yielding line Beinong6. The map contains 2431 SNPs and 128 SSR & EST-SSR markers in a total coverage of 3213.2 cM with an average interval of 1.26 cM per marker. Eighty-eight QTLs for thousand-grain weight (TGW), grain length (GL), grain width (GW) and grain thickness (GT) were detected in nine ecological environments (Beijing, Shijiazhuang and Kaifeng) during five years between 2010–2014 by inclusive composite interval mapping (ICIM) (LOD≥2.5). Among which, 17 QTLs for TGW were mapped on chromosomes 1A, 1B, 2A, 2B, 3A, 3B, 3D, 4A, 4D, 5A, 5B and 6B with phenotypic variations ranging from 2.62% to 12.08%. Four stable QTLs for TGW could be detected in five and seven environments, respectively. Thirty-two QTLs for GL were mapped on chromosomes 1B, 1D, 2A, 2B, 2D, 3B, 3D, 4A, 4B, 4D, 5A, 5B, 6B, 7A and 7B, with phenotypic variations ranging from 2.62% to 44.39%. QGl.cau-2A.2 can be detected in all the environments with the largest phenotypic variations, indicating that it is a major and stable QTL. For GW, 12 QTLs were identified with phenotypic variations range from 3.69% to 12.30%. We found 27 QTLs for GT with phenotypic variations ranged from 2.55% to 36.42%. In particular, QTL QGt.cau-5A.1 with phenotypic variations of 6.82–23.59% was detected in all the nine environments. Moreover, pleiotropic effects were detected for several QTL loci responsible for grain shape and size that could serve as target regions for fine mapping and marker assisted selection in wheat breeding programs.     

Construction of Chromosome Segment Substitution Lines in Peanut (Arachis hypogaea L.) Using a Wild Synthetic and QTL Mapping for Plant Morphology

Chromosome segment substitution lines (CSSLs) are powerful QTL mapping populations that have been used to elucidate the molecular basis of interesting traits of wild species. Cultivated peanut is an allotetraploid with limited genetic diversity. Capturing the genetic diversity from peanut wild relatives is an important objective in many peanut breeding programs. In this study, we used a marker-assisted backcrossing strategy to produce a population of 122 CSSLs from the cross between the wild synthetic allotetraploid (A. ipaënsis×A. duranensis)^4x and the cultivated Fleur11 variety. The 122 CSSLs offered a broad coverage of the peanut genome, with target wild chromosome segments averaging 39.2 cM in length. As a demonstration of the utility of these lines, four traits were evaluated in a subset of 80 CSSLs. A total of 28 lines showed significant differences from Fleur11. The line×trait significant associations were assigned to 42 QTLs: 14 for plant growth habit, 15 for height of the main stem, 12 for plant spread and one for flower color. Among the 42 QTLs, 37 were assigned to genomic regions and three QTL positions were considered putative. One important finding arising from this QTL analysis is that peanut growth habit is a complex trait that is governed by several QTLs with different effects. The CSSL population developed in this study has proved efficient for deciphering the molecular basis of trait variations and will be useful to the peanut scientific community for future QTL mapping studies.     

High Resolution Consensus Mapping of Quantitative Trait Loci for Fiber Strength,Length and Micronaire on Chromosome 25 of the Upland Cotton (Gossypium hirsutum L.)

Cotton (Gossypium hirsutum L.) is an important agricultural crop that provides renewable natural fiber resources for the global textile industry. Technological developments in the textile industry and improvements in human living standards have increased the requirement for supplies and better quality cotton. Upland cotton 0–153 is an elite cultivar harboring strong fiber strength genes. To conduct quantitative trait locus (QTL) mapping for fiber quality in 0–153, we developed a population of 196 recombinant inbred lines (RILs) from a cross between 0–153 and sGK9708. The fiber quality traits in 11 environments were measured and a genetic linkage map of chromosome 25 comprising 210 loci was constructed using this RIL population, mainly using simple sequence repeat markers and single nucleotide polymorphism markers. QTLs were identified across diverse environments using the composite interval mapping method. A total of 37 QTLs for fiber quality traits were identified on chromosome 25, of which 17 were stably expressed in at least in two environments. A stable fiber strength QTL, qFS-chr25-4, which was detected in seven environments and was located in the marker interval between CRI-SNP120491 and BNL2572, could explain 6.53%–11.83% of the observed phenotypic variations. Meta-analysis also confirmed the above QTLs with previous reports. Application of these QTLs could contribute to improving fiber quality and provide information for marker-assisted selection.     

A High-Density Genetic Map Identifies a Novel Major QTL for Boron Efficiency in Oilseed Rape (Brassica napus L.)

Low boron (B) seriously limits the growth of oilseed rape (Brassica napus L.), a high B demand species that is sensitive to low B conditions. Significant genotypic variations in response to B deficiency have been observed among B. napus cultivars. To reveal the genetic basis for B efficiency in B. napus, quantitative trait loci (QTLs) for the plant growth traits, B uptake traits and the B efficiency coefficient (BEC) were analyzed using a doubled haploid (DH) population derived from a cross between a B-efficient parent, Qingyou 10, and a B-inefficient parent, Westar 10. A high-density genetic map was constructed based on single nucleotide polymorphisms (SNPs) assayed using Brassica 60 K Infinium BeadChip Array, simple sequence repeats (SSRs) and amplified fragment length polymorphisms (AFLPs). The linkage map covered a total length of 2139.5 cM, with 19 linkage groups (LGs) and an average distance of 1.6 cM between adjacent markers. Based on hydroponic evaluation of six B efficiency traits measured in three separate repeated trials, a total of 52 QTLs were identified, accounting for 6.14–46.27% of the phenotypic variation. A major QTL for BEC, qBEC-A3a, was co-located on A3 with other QTLs for plant growth and B uptake traits under low B stress. Using a subset of substitution lines, qBEC-A3a was validated and narrowed down to the interval between CNU384 and BnGMS436. The results of this study provide a novel major locus located on A3 for B efficiency in B. napus that will be suitable for fine mapping and marker-assisted selection breeding for B efficiency in B. napus.     

Mapping QTLs for mineral accumulation and shoot dry biomass under different Zn nutritional conditions in Chinese cabbage (Brassica rapa L. ssp. pekinensis)

Chinese cabbage (Brassica rapa L. ssp. pekinensis) is one of the most important vegetables in China. Genetic dissection of leaf mineral accumulation and tolerance to Zn stress is important for the improvement of the nutritional quality of Chinese cabbage by breeding. A mapping population with 183 doubled haploid (DH) lines was used to study the genetics of mineral accumulation and the growth response to Zn. The genetic map was constructed based on 203 AFLPs, 58 SSRs, 22 SRAPs and four ESTPs. The concentration of 11 minerals was determined in leaves for 142 DH lines grown in an open field. In addition shoot dry biomass (SDB) under normal, deficient and excessive Zn nutritional conditions were investigated in hydroponics experiments. Ten QTLs, each explaining 11.1–17.1% of the Na, Mg, P, Al, Fe, Mn, Zn and Sr concentration variance, were identified by multiple-QTL model (MQM) mapping. One common QTL was found affecting SDB under normal, deficient and excessive Zn nutritional conditions. An additional QTL was detected for SDB under Zn excess stress only. These results offer insights into the genetic basis of leaf mineral accumulation and plant growth under Zn stress conditions in Chinese cabbage.     

Genome-wide SNP identification for the construction of a high-resolution genetic map of Japanese flounder (Paralichthys olivaceus): applications to QTL mapping of Vibrio anguillarum disease resistance and comparative genomic analysis

High-resolution genetic maps are essential for fine mapping of complex traits, genome assembly, and comparative genomic analysis. Single-nucleotide polymorphisms (SNPs) are the primary molecular markers used for genetic map construction. In this study, we identified 13,362 SNPs evenly distributed across the Japanese flounder (Paralichthys olivaceus) genome. Of these SNPs, 12,712 high-confidence SNPs were subjected to high-throughput genotyping and assigned to 24 consensus linkage groups (LGs). The total length of the genetic linkage map was 3,497.29 cM with an average distance of 0.47 cM between loci, thereby representing the densest genetic map currently reported for Japanese flounder. Nine positive quantitative trait loci (QTLs) forming two main clusters for Vibrio anguillarum disease resistance were detected. All QTLs could explain 5.1–8.38% of the total phenotypic variation. Synteny analysis of the QTL regions on the genome assembly revealed 12 immune-related genes, among them 4 genes strongly associated with V. anguillarum disease resistance. In addition, 246 genome assembly scaffolds with an average size of 21.79 Mb were anchored onto the LGs; these scaffolds, comprising 522.99 Mb, represented 95.78% of assembled genomic sequences. The mapped assembly scaffolds in Japanese flounder were used for genome synteny analyses against zebrafish (Danio rerio) and medaka (Oryzias latipes). Flounder and medaka were found to possess almost one-to-one synteny, whereas flounder and zebrafish exhibited a multi-syntenic correspondence. The newly developed high-resolution genetic map, which will facilitate QTL mapping, scaffold assembly, and genome synteny analysis of Japanese flounder, marks a milestone in the ongoing genome project for this species.     

QTL Analysis of Popping Fold and the Consistency of QTLs Under Two Environments in Popcorn

Popping fold (PF) is the most important quality trait in popcorn. In this study, a total of 259 F_2:3 families, derived from the cross between a dent corn inbred Dan232 and a popcorn inbred N04, were evaluated for their popping folds in replicated experiments under two environments. Of 613 simple sequence repeat (SSR) primer pairs screened, 183 pairs were selected to construct a genetic linkage map with the genetic distance of 1 762.2 cM (centimorgan) and on average 9.63 cM every marker. Quantative trait loci (QTL) were identified, and their genetic effects were estimated using CIM (composite interval mapping) method. The interactions among QTLs detected were calculated using MIM (multiple interval mapping) method. In all, 22 QTLs were detected, and only 5 of them were common under two environments. Contribution to phenotypic variation of a single QTL varied from 3.07% to 12.84%, and total contributions of all QTLs under two environments were 66.46% and 51.90%, respectively. Three QTLs (qPF-6-1, qPF-8-1 and qPF-1-3) with more than 10% contributions were observed. The additive effects were larger than dominant effects for most QTLs. The amount of QTLs showing additive, partially dominant, dominant and over-dominant effects were 4, 5, 0, 2 in spring sowing and 2, 5, 2, 2 in summer sowing, respectively. There were only 2.60% pairs of QTLs or maker intervals expressing AA, DA or DD interactions.     

GBS-SNP and SSR based genetic mapping and QTL analysis for drought tolerance in upland cotton

A recombinant inbred line mapping population of intra-species upland cotton was generated from a cross between the drought-tolerant female parent (AS2) and the susceptible male parent (MCU13). A linkage map was constructed deploying 1,116 GBS-based SNPs and public domain-based 782 SSRs spanning a total genetic distance of 28,083.03 cM with an average chromosomal span length of 1,080.12 cM with inter-marker distance of 10.19 cM.A total of 19 quantitative trait loci (QTLs) were identified in nine chromosomes for field drought tolerance traits. Chromosomes 3 and 8 harbored important drought tolerant QTLs for chlorophyll stability index trait while for relative water content trait, three QTLs on chromosome 8 and one QTL each on chromosome 4, 12 were identified. One QTL on each chromosome 8, 5, and 7, and two QTLs on chromosome 15 linking to proline content were identified. For the nitrate reductase activity trait, two QTLs were identified on chromosome 3 and one on each chromosome 8, 13, and 26. To complement our QTL study, a meta-analysis was conducted along with the public domain database and resulted in a consensus map for chromosome 8. Under field drought stress, chromosome 8 harbored a drought tolerance QTL hotspot with two in-house QTLs for chlorophyll stability index (qCSI01, qCSI02) and three public domain QTLs (qLP.FDT_1, qLP.FDT_2, qCC.ST_3). Identified QTL hotspot on chromosome 8 could play a crucial role in exploring abiotic stress-associated genes/alleles for drought trait improvement.Supplementary InformationThe online version contains supplementary material available at 10.1007/s12298-021-01041-y.     

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.     

Exploring the Genetic Characteristics of Two Recombinant Inbred Line Populations via High-Density SNP Markers in Maize

Understanding genetic characteristics can reveal the genetic diversity in maize and be used to explore evolutionary mechanisms and gene cloning. A high-density linkage map was constructed to determine recombination rates (RRs), segregation distortion regions (SDRs), and recombinant blocks (RBs) in two recombinant inbred line populations (RILs) (B73/By804 and Zong3/87-1) generated by the single seed descent method. Population B73/By804 containing 174 lines were genotyped with 198 simple sequence repeats (SSRs) markers while population Zong3/87-1 comprised of 175 lines, were genotyped with 210 SSR markers along with 1536 single nucleotide polymorphism (SNP) markers for each population, spanning 1526.7 cM and 1996.2 cM in the B73/By804 and Zong3/87-1 populations, respectively. The total variance of the RR in the whole genome was nearly 100 fold, and the maximum average was 10.43–11.50 cM/Mb while the minimum was 0.08–0.10 cM/Mb in the two populations. The average number of RB was 44 and 37 in the Zong3/87-1 and B73/By804 populations, respectively, whereas 28 SDRs were observed in both populations. We investigated 11 traits in Zong3/87-1 and 10 traits in B73/By804. Quantitative trait locus (QTLs) mapping of SNP+SSR with SNP and SSR marker sets were compared to showed the impact of different density markers on QTL mapping and resolution. The confidence interval of QTL Pa19 (FatB gene controlling palmitic acid content) was reduced from 3.5 Mb to 1.72 Mb, and the QTL Oil6 (DGAT1-2 gene controlling oil concentration) was significantly reduced from 10.8 Mb to 1.62 Mb. Thus, the use of high-density markers considerably improved QTL mapping resolution. The genetic information resulting from this study will support forthcoming efforts to understand recombination events, SDRs, and variations among different germplasm. Furthermore, this study will facilitate gene cloning and understanding of the fundamental sources of total variation and RR in maize, which is the most widely cultivated cereal crop.     

Genotyping-by-sequencing map permits identification of clubroot resistance QTLs and revision of the reference genome assembly in cabbage (Brassica oleracea L.)

Clubroot is a devastating disease caused by Plasmodiophora brassicae and results in severe losses of yield and quality in Brassica crops. Many clubroot resistance genes and markers are available in Brassica rapa but less is known in Brassica oleracea. Here, we applied the genotyping-by-sequencing (GBS) technique to construct a high-resolution genetic map and identify clubroot resistance (CR) genes. A total of 43,821 SNPs were identified using GBS data for two parental lines, one resistant and one susceptible lines to clubroot, and 18,187 of them showed >5× coverage in the GBS data. Among those, 4,103 were credibly genotyped for all 78 F₂ individual plants. These markers were clustered into nine linkage groups spanning 879.9 cM with an average interval of 1.15 cM. Quantitative trait loci (QTLs) survey based on three rounds of clubroot resistance tests using F_{2 : 3} progenies revealed two and single major QTLs for Race 2 and Race 9 of P. brassicae, respectively. The QTLs show similar locations to the previously reported CR loci for Race 4 in B. oleracea but are in different positions from any of the CR loci found in B. rapa. We utilized two reference genome sequences in this study. The high-resolution genetic map developed herein allowed us to reposition 37 and 2 misanchored scaffolds in the 02–12 and TO1000DH genome sequences, respectively. Our data also support additional positioning of two unanchored 3.3 Mb scaffolds into the 02–12 genome sequence.     

Genome-wide insertion–deletion (InDel) marker discovery and genotyping for genomics-assisted breeding applications in chickpea

We developed 21,499 genome-wide insertion–deletion (InDel) markers (2- to 54-bp in silico fragment length polymorphism) by comparing the genomic sequences of four (desi, kabuli and wild C. reticulatum) chickpea [Cicer arietinum (L.)] accessions. InDel markers showing 2- to 6-bp fragment length polymorphism among accessions were abundant (76.8%) in the chickpea genome. The physically mapped 7,643 and 13,856 markers on eight chromosomes and unanchored scaffolds, respectively, were structurally and functionally annotated. The 4,506 coding (23% large-effect frameshift mutations) and regulatory InDel markers were identified from 3,228 genes (representing 11.7% of total 27,571 desi genes), suggesting their functional relevance for trait association/genetic mapping. High amplification (97%) and intra-specific polymorphic (60–83%) potential and wider genetic diversity (15–89%) were detected by genome-wide 6,254 InDel markers among desi, kabuli and wild accessions using even a simpler cost-effective agarose gel-based assay. This signifies added advantages of this user-friendly genetic marker system for manifold large-scale genotyping applications in laboratories with limited infrastructure and resources. Utilizing 6,254 InDel markers-based high-density (inter-marker distance: 0.212 cM) inter-specific genetic linkage map (ICC 4958 × ICC 17160) of chickpea as a reference, three major genomic regions harboring six flowering and maturity time robust QTLs (16.4–27.5% phenotypic variation explained, 8.1–11.5 logarithm of odds) were identified. Integration of genetic and physical maps at these target QTL intervals mapped on three chromosomes delineated five InDel markers-containing candidate genes tightly linked to the QTLs governing flowering and maturity time in chickpea. Taken together, our study demonstrated the practical utility of developing and high-throughput genotyping of such beneficial InDel markers at a genome-wide scale to expedite genomics-assisted breeding applications in chickpea.     

Construction of Three High-Density Genetic Linkage Maps and Dynamic QTL Mapping of Growth Traits in Yellow River Carp (Cyprinus carpio haematopterus)

To provide the theoretical basis for researching growth, development, and molecular marker-assisted breeding of the economically important Yellow River carp (Cyprinus carpio haematopterus) using dynamic quantitative trait locus (QTL) mapping, we constructed three genetic linkage maps from 207 progeny using a new modified genotyping-by-sequencing method. The three maps contained 16,886, 16,548, and 7482 single nucleotide polymorphism markers, respectively, with an average interval of 0.36 cM, 0.45 cM, and 1.00 cM. We identified 148 QTLs related to four growth traits that were located on 25 chromosomes from three growth stages of Yellow River carp. A total of 32, 36, 43, and 37 QTLs were associated with body length, height, width, and weight, respectively. Among them, 47 QTLs were detected for only one growth trait in one stage, but all of the other QTLs were co-localized. Of the 14 main QTLs, 13 were located on chromosome 12, which suggests the presence of growth-related genes on this chromosome. We then detected 17 candidate genes within 50 K upstream and downstream of the 14 main QTLs. This is the first report of the dynamic QTL mapping of growth traits of Yellow River carp, and the results can be used in future studies of growth, development, and molecular-assisted breeding of this species.     

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

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