High-density Genetic Linkage Map Research Articles

Haplogenome assembly reveals structural variation in Eucalyptus interspecific hybrids.

De novo phased (haplo)genome assembly using long-read DNA sequencing data has improved the detection and characterization of structural variants (SVs) in plant and animal genomes. Able to span across haplotypes, long reads allow phased, haplogenome assembly in highly outbred organisms such as forest trees. Eucalyptus tree species and interspecific hybrids are the most widely planted hardwood trees with F1 hybrids of Eucalyptus grandis and E. urophylla forming the bulk of fast-growing pulpwood plantations in subtropical regions. The extent of structural variation and its effect on interspecific hybridization is unknown in these trees. As a first step towards elucidating the extent of structural variation between the genomes of E. grandis and E. urophylla, we sequenced and assembled the haplogenomes contained in an F1 hybrid of the two species. Using Nanopore sequencing and a trio-binning approach, we assembled the separate haplogenomes (566.7 Mb and 544.5 Mb) to 98.0% BUSCO completion. High-density SNP genetic linkage maps of both parents allowed scaffolding of 88.0% of the haplogenome contigs into 11 pseudo-chromosomes (scaffold N50 of 43.8 Mb and 42.5 Mb for the E. grandis and E. urophylla haplogenomes, respectively). We identify 48,729 SVs between the two haplogenomes providing the first detailed insight into genome structural rearrangement in these species. The two haplogenomes have similar gene content, 35,572 and 33,915 functionally annotated genes, of which 34.7% are contained in genome rearrangements. Knowledge of SV and haplotype diversity in the two species will form the basis for understanding the genetic basis of hybrid superiority in these trees.

Quantitative trait locus mapping for important yield traits of a sorghum-sudangrass hybrid using a high-density single nucleotide polymorphism map.

The sorghum-sudangrass hybrid is a vital gramineous herbage.The F2 population was obtained to clarify genetic regularities among the traits of sorghum-sudangrass hybrids by bagging and selfing in the F1 generation using 'scattered ear sorghum' and 'red hull sudangrass.' This hybrid combines the characteristics of the strong resistance of parents, high yield, and good palatability and has clear heterosis. A thorough understanding of the genetic mechanisms of yield traits in sorghum-sudangrass hybrids is essential in improving their yield. Therefore, we conducted quantitative trait locus (QTL) mapping for plant height, stem diameter, tiller number, leaf number, leaf length, leaf width, and fresh weight of each plant in three different environments, using a high-density genetic linkage map based on single nucleotide polymorphism markers previously constructed by our team. A total of 55 QTLs were detected, uniformly distributed over the 10 linkage groups (LGs), with logarithm of odds values ranging between 2.5 and 7.1, which could explain the 4.9-52.44% phenotypic variation. Furthermore, 17 yield-related relatively high-frequency QTL (RHF-QTL) loci were repeatedly detected in at least two environments, with an explanatory phenotypic variation of 4.9-30.97%. No RHF-QTLs were associated with the tiller number. The genes within the confidence interval of RHF-QTL were annotated, and seven candidate genes related to yield traits were screened. Three QTL sites overlapping or adjacent to previous studies were detected by comparative analysis. We also found that QTL was enriched and that qLL-10-1 and qFW-10-4 were located at the same location of 25.81 cM on LG10. The results of this study provide a foundation for QTL fine mapping, candidate gene cloning, and molecular marker-assisted breeding of sorghum-sudangrass hybrids.

QTL mapping of yield components and kernel traits in wheat cultivars TAM 112 and Duster.

In the Southern Great Plains, wheat cultivars have been selected for a combination of outstanding yield and drought tolerance as a long-term breeding goal. To understand the underlying genetic mechanisms, this study aimed to dissect the quantitative trait loci (QTL) associated with yield components and kernel traits in two wheat cultivars `TAM 112' and `Duster' under both irrigated and dryland environments. A set of 182 recombined inbred lines (RIL) derived from the cross of TAM 112/Duster were planted in 13 diverse environments for evaluation of 18 yield and kernel related traits. High-density genetic linkage map was constructed using 5,081 single nucleotide polymorphisms (SNPs) from genotyping-by-sequencing (GBS). QTL mapping analysis detected 134 QTL regions on all 21 wheat chromosomes, including 30 pleiotropic QTL regions and 21 consistent QTL regions, with 10 QTL regions in common. Three major pleiotropic QTL on the short arms of chromosomes 2B (57.5 - 61.6 Mbps), 2D (37.1 - 38.7 Mbps), and 7D (66.0 - 69.2 Mbps) colocalized with genes Ppd-B1, Ppd-D1, and FT-D1, respectively. And four consistent QTL associated with kernel length (KLEN), thousand kernel weight (TKW), plot grain yield (YLD), and kernel spike-1 (KPS) (Qklen.tamu.1A.325, Qtkw.tamu.2B.137, Qyld.tamu.2D.3, and Qkps.tamu.6A.113) explained more than 5% of the phenotypic variation. QTL Qklen.tamu.1A.325 is a novel QTL with consistent effects under all tested environments. Marker haplotype analysis indicated the QTL combinations significantly increased yield and kernel traits. QTL and the linked markers identified in this study will facilitate future marker-assisted selection (MAS) for pyramiding the favorable alleles and QTL map-based cloning.

Construction of a high-density SSR genetic linkage map and identification of QTL for storage-root yield and dry-matter content in sweetpotato

Sweetpotato (Ipomoea batatas (L.) Lam.) is a widely grown food crop especially in developing countries. Increasing storage-root yield and dry-matter content has been the main breeding objective of the crop, and DNA marker-assisted breeding is needed for this purpose. In this study, using a mapping population of 500 F1 individuals from a cross between Xushu 18 (female) and Xu 781 (male), we constructed a high-density genetic linkage map of sweetpotato using 601 simple-sequence repeat (SSR) primer pairs. The Xushu 18 map contained 90 linkage groups with 5547 SSR markers and spanned 18,263.5 cM, and the Xu 781 map contained 90 linkage groups with 4599 SSR markers and spanned 18,043.7 cM, representing the highest genome coverage yet reported for sweetpotato. We identified 33 QTL for storage-root yield and 16 QTL for dry-matter content, explaining respectively 6.5%–47.5% and 3.2%–18.9% of variation. These results provide a foundation for fine-mapping and cloning of QTL and for marker-assisted breeding in sweetpotato.

High-Density Genetic Linkage Map of the Southern Blue-ringed Octopus (Octopodidae: Hapalochlaena maculosa)

Genetic linkage maps provide a useful resource for non-model genomes and can aid in genome reassembly to form more contiguous pseudo-chromosomes. We present the first linkage map of any cephalopod, H. maculosa, composed of 47 linkage groups (LG). A total of 2166 single nucleotide polymorphisms and 2455 presence–absence variant loci were utilised by Lep-Map3 in linkage map construction. The map length spans 2016.62 cM with an average marker distance of 0.85 cM. Integration of the recent H. maculosa genome allowed 1151 scaffolds comprising 34% of the total genomic sequence to be orientated and/or placed using 1278 markers across all 47 LG. The linkage map generated provides a new perspective on HOX gene distribution in octopods. In the H. maculosa linkage map three (SCR, LOX4 and POST1) of six identified HOX genes (HOX1/LAB, SCR, LOX2, LOX4, LOX5, POST1) were located within the same LG (LG 9). The generation of a linkage map for H. maculosa has provided a valuable resource for understanding the evolution of cephalopod genomes and will provide a base for future work.

Construction of High-Density Genetic Linkage Map Using GBS-SNPs and SSRs in Interspecific Hybrid Derived from the Cross Between ‘Manpungbae’ and ‘Oharabeni’ Pear (Pyrus spp.)

Construction of High-Density Genetic Linkage Map Using GBS-SNPs and SSRs in Interspecific Hybrid Derived from the Cross Between ‘Manpungbae’ and ‘Oharabeni’ Pear (<i>Pyrus</i> spp.)

Identification of a genomic region linked with sex determination of Undaria pinnatifida (Alariaceae) through genomic resequencing and genetic linkage analyses of a segregating gametophyte family.

Different from the traditional knowledge about kelp, three sexual phenotypes (female, male, and monoecious) exist in the haploid gametophytes of Undaria pinnatifida. However, the sex-determining mechanisms remain unknown. Genetic linkage mapping is an efficient tool to identify sex-linked regions. In the present study, we resequenced a segregating gametophyte family based on the male genome of U. pinnatifida. A high-density genetic linkage map was constructed using 9887 SNPs, with an average distance of 0.41 cM between adjacent SNPs. On the basis of this genetic map and using the composite interval mapping method, we identified 62 SNPs significantly linked with the sexual phenotype. They were located at a position of 67.67 cM on the linkage group 23, corresponding to a physical range of 14.67 Mbp on the HiC_Scaffold_23 of the genome. Reanalysis of the previous specific length amplified fragment sequencing data according to the reference genome led to the identification of a sex-linked genomic region that encompassed the above-mentioned 14.67 Mbp region. Hence, this overlapped genomic range was likely the sex-determining region. Within this region, 129 genes were retrieved and 39 of them were annotated with explicit function, including the potential male sex-determining gene-encoding high mobility group (HMG) domain protein. Relative expression analysis of the HMG gene showed that its expression was higher in male gametophytes during the vegetative phase and monoecious gametophytes during both the vegetative and gametogenesis phases, but significantly lower in male gametophytes during the gametogenesis phase. These results provide a foundation for deciphering the sex-determining mechanism of U. pinnatifida.

QTL Analysis and CAPS Marker Development Linked with Russet in Pear (Pyrus spp.).

The fruit skin types of pear (Pyrus spp.) are divided into russet, smooth, and intermediate. One of the important traits in pear breeding programs is russet on pear fruit skin because it affects the commercial value. In the present study, a high-density genetic linkage map of ‘Whangkeumbae’ (smooth) × ‘Minibae’ (russet) was constructed. In addition, quantitative trait loci (QTL) analysis was performed to identify russet related QTL and develop a cleaved amplified polymorphism sequence (CAPS) marker. Together with SNPs derived from Axiom Pear 70K Genotyping Array and genotyping-by-sequencing derived SNPs and SSRs generated in previous study, an integrated genetic linkage map of ‘Whangkeumbae’ × ‘Minibae’ was constructed. A total of 1263 markers were anchored in 17 linkage groups (LGs) with a total genetic distance of 1894.02 cM and an average marker density of 1.48 cM. The chromosome coverage of ‘Whangkeumbae’ × ‘Minibae’ map was improved because the SNPs derived from Axiom Pear 70K Genotyping Array were anchored. QTL analysis was performed using previous russet phenotype data evaluated with russet coverage and Hunter a. As a result of QTL analysis, russet coverage- and Hunter a-related QTLs were identified in LG8 of the ‘Whangkeumbae’ × ‘Minibae’ map, and SNPs located in the QTL region were heterozygous in the ‘Minibae’. Although the russet coverage- and Hunter a-related QTLs were commonly detected in LG8, the logarithm of odds values of SNPs in the QTL region were higher in QTL related to russet coverage than to Hunter a. The CAPS marker (CBp08ca01) was developed using an array SNP located in the russet coverage related QTL, and the genotype of CBp08ca01 showed a 1:1 ratio in ‘Whangkeumbae’ × ‘Minibae’ (χ2 = 0.65, p > 0.05). ‘Whangkeumbae’ and ‘Minibae’ were thought to have rr and Rr genotypes, respectively, and the genetic factors controlling the russet formation might be located in chromosome 8. The CBp08ca01 was able to select F1 individuals with less than 30% russet coverage. Thus, it will be a useful tool for marker-assisted selection in pears.

QTL mapping reveals candidate genes for main agronomic traits in Luffa based on a high-resolution genetic map.

Luffa is an important medicinal and edible vegetable crop of Cucurbitaceae. Strong heterosis effects and strikingly complementary characteristics were found between the two domesticated Luffa cultivars, Luffa acutangula and Luffa cylindrica. To explore the genetic basis underlying their important agronomic traits, we constructed the first interspecific high-density genetic linkage map using a BC1 population of 110 lines derived from a cross between S1174 (Luffa acutangula) and P93075 (Luffa cylindrica). The map spanned a total of 2246.74 cM with an average distance of 0.48 cM between adjacent markers. Thereafter, a large-scale field-based quantitative trait loci (QTLs) mapping was conducted for 25 important agronomic traits and 40 significant genetic loci distributed across 11 chromosomes were detected. Notably, a vital QTL (qID2) located on chromosome 9 with a minimum distance of 23 kb was identified to be responsible for the internode diameter and explained 11% of the phenotypic variation. Lac09g006860 (LacCRWN3), encoding a nuclear lamina protein involved in the control of nuclear morphology, was the only gene harbored in qID2. Sequence alignment showed completely different promoter sequences between the two parental alleles of LacCRWN3 except for some nonsynonymous single nucleotide polymorphisms (SNPs) in exons, and the expression level in thick-stem P93075 was distinctively higher than that in thin-stem S1174. According to the natural variation analysis of a population of 183 inbred lines, two main haplotypes were found for LacCRWN3: the P93075-like and S1174-like, with the former haplotype lines exhibiting significantly thicker internode diameters than those of the latter haplotype lines. It showed that LacCRWN3, as the only CRWN3 gene in Cucurbitaceae, was the most likely candidate gene regulating the internode diameter of Luffa. Our findings will be beneficial for deciphering the molecular mechanism of key phenotypic traits and promoting maker-assisted breeding in Luffa.

SNP-based high-density linkage map construction and QTL mapping of black spot disease resistance in Chinese sand pear.

Black spot disease (PBS) caused by Alternaria alternata is an economic disease of pear (Pyrus pyrifolia Nakai). Developing cultivars with durable PBS resistance traits is an important research objective for improving pear germplasm. The Deshengxiang is a popular pear variety in China and resistant to PBS. This study aimed to detect quantitative trait loci (QTL) associated with PBS resistance trait in pear and determine closely linked molecular markers by specific locus amplified fragment sequencing (SLAF-seq). F1 population resulting from a cross between "Deshengxiang" (female) and "Guiguan," a susceptible (male) variety, was developed and evaluated in 2016 and 2017. SLAF technology was used to discover SNPs in the F1 individuals and subsequently a high-density genetic linkage map for PBS resistance was constructed which contained 17,604 SNP markers. Based on the linkage map, the markers were distributed into 17 linkage groups, spanning 1548.48cM, with a mean marker distance of 0.09cM, representing the densest genetic map of the genus Pyrus. QTL analysis of PBS resistance identified a locus strongly related to PBS resistance at 77.68 ~ 112.99cM on linkage group 15, which was further narrowed down to 93.79 ~ 112.99cM. Two markers, Marker94293 and Marker94206, located at 97.47 and 102.93cM, were closely associated with PBS resistance, with a Δ (SNP index) value of 0.46. Co-localization of QTL interval, bioinformatics analysis, and functional annotation revealed PBS putative candidate genes. Overall, the high-density pear linkage map is a suitable reference for mapping PBS resistance trait, QTL, and genes identified in this study contribute information that could be useful for PBS improvement in pear.

Genome-wide QTL mapping and RNA-seq reveal the genetic variation influencing growth traits in giant grouper (Epinephelus lanceolatus)

Genetic improvement of growth traits is a major target of grouper aquaculture and breeding. As one of the largest groupers, the giant grouper (Epinephelus lanceolatus) has excellent growth performance, although the genetic basis of its growth traits has been rarely studied. In this study, we successfully constructed a high-density genetic linkage map with 2988 SNPs generated by genotype-by-sequencing of 178 individuals, which belong to an F1 full-sibling family. The length of the map was 3231.5 cM with an average interval of 1.21 cM. Then, we performed genome-wide QTL (quantitative trait locus) mapping for five growth traits including all length, body length, body height, body thickness, and body weight in the giant grouper and identified six growth-associated QTLs, which explained 4.65–12.56% of the phenotypic variance. These QTLs were distributed on five linkage groupers (LGs) of our sex-averaged linkage map with two QTLs on LG11, four QTLs on LG7, LG10, LG15, and LG23. The genes identified within the significant QTLs were validated using qPCR and the results showed six significantly upregulated genes (kalrn, ypel1, supt7l, lacs5, ccnd2, mybpc2) in tissues (muscle, fat, liver, gill, etc.) of the fast vs slow growth groups were highlighted as promising candidates. Further, RNA-seq analysis revealed 484 differentially expressed genes (DEGs) between fast/slow growth groups that play roles in the RNA transport, metabolic pathways, PPAR signaling pathway, and carbon metabolism pathways. Notably, 27 DEGs were detected in the identified growth-associated-QTL regions. Those candidate genes shared between QTL mapping and DEGs may play important roles in regulating cell growth, signal transduction, carbohydrate metabolism and skeletal development. Overall, our findings are useful for improving the genetic process for molecular marker-assisted selection and provide new insights into elucidating the molecular mechanism of growth variation in this species.

Isolation and identification of SiCOL5, which is involved in photoperiod response, based on the quantitative trait locus mapping of Setaria italica.

Foxtail millet (Setaria italica) is a versatile grain and fodder crop grown in arid and semi-arid regions. It is an especially important crop for combating malnutrition in certain poverty-stricken areas of the world. Photoperiod sensitivity is a major constraint to the distribution and utilization of foxtail millet germplasm resources. Foxtail millet may be suitable as a model species for studying the photoperiod sensitivity of C4 crops. However, the genetic basis of the photoperiod response of foxtail millet remains poorly studied. To detect the genetic basis of photoperiod sensitivity-related traits, a recombinant inbred line (RIL) population consisting of 313 lines derived from a cross between the spring-sown cultivar “Longgu 3” and the summer-sown cultivar “Canggu 3” was established. The RIL population was genotyped using whole-genome re-sequencing and was phenotyped in four environments. A high-density genetic linkage map was constructed with an average distance between adjacent markers of 0.69 cM. A total of 21 quantitative trait loci (QTLs) were identified by composite interval mapping, and 116 candidate genes were predicted according to gene annotations and variations between parents, among which three genes were considered important candidate genes by the integration and overall consideration of the results from gene annotation, SNP and indel analysis, cis-element analysis, and the expression pattern of different genes in different varieties, which have different photoperiod sensitivities. A putative candidate gene, SiCOL5, was isolated based on QTL mapping analysis. The expression of SiCOL5 was sensitive to photoperiod and was regulated by biological rhythm-related genes. Function analysis suggested that SiCOL5 positively regulated flowering time. Yeast two-hybrid and bimolecular fluorescence complementation assays showed that SiCOL5 was capable of interacting with SiNF-YA1 in the nucleus.

A genetic linkage map of the Pacific white shrimp (Litopenaeus vannamei): QTL mapping for low-temperature tolerance and growth-related traits and identification of the candidate genes

Low water temperature is a prevailing abiotic stress which adversely impacts global shrimp growth and production. In this study, a high-density genetic linkage map of L. vannamei was constructed using double-digest restriction site-associated DNA sequencing (ddRAD-seq) with an F1 full-sib family mapping panel comprising 148 progenies and 2 parents. A total of 2528 single-nucleotide polymorphisms (SNPs) were assigned to 48 linkage groups (LGs), with a total genetic map length of 3227.383 centimorgans (cM) and an inter-locus density of 0.783 cM/locus. The number of markers per LG ranged from 12 to 190, with a mean of 56. The length of LGs varied from 15.07 to 158.314 cM, with a mean length of 67.237 cM. Five quantitative trait loci (QTLs) for low-temperature tolerance with a logarithm of odds (LOD) threshold≥2.5 were detected, of which only one was identified based on a linkage group-wide significant LOD threshold. Notably, two growth-trait (body weight) related QTLs were located on LG36 with a genome-wide significant LOD threshold. According to the genome and relevant annotations of L. vannamei, a major growth-related candidate gene, tRNA methyltransferase 10 homolog A (TRMT10A), was identified from genomic scaffolds. Further analysis demonstrated that four linked missense mutation SNPs within TRMT10A were closely related to the body weight. Taken together, the constructed genetic linkage map under low-temperature stress provides a valuable reference for QTL mapping and future genomic studies. Its application can facilitate comparative mapping with other populations, as well as marker-assisted selection (MAS) breeding of L. vannamei.

Using a high density bin map to analyze quantitative trait locis of germination ability of maize at low temperatures.

Low temperatures in the spring often lead to a decline in the emergence rate and uniformity of maize, which can affect yield in northern regions. This study used 365 recombinant inbred lines (RILs), which arose from crossing Qi319 and Ye478, to identify low-temperature resistance during the germination stage by measuring eight low-temperature-related traits. The quantitative trait locis (QTLs) were mapped using R/qtl software by combining phenotypic data, and the genotyping by sequencing (GBS) method to produce a high-density genetic linkage map. Twenty QTLs were detected during QTL mapping, of which seven QTLs simultaneously detected a consistent 197.10–202.30 Mb segment on chromosome 1. The primary segment was named cQTL1-2, with a phenotypic variation of 5.18–25.96% and a physical distance of 5.2 Mb. This combines the phenotype and genotype with the identification of seven chromosome segment substitution lines (CSSLs), which were derived from Ye478*Qi319 and related to cQTL1-2. The physical distance of cQTL1-2 was reduced to approximately 1.9 Mb. The consistent meta-QTL mQTL1 was located at 619.06 cM on chromosome 1, had a genetic distance of 7.27 cM, and overlapped with cQTL1-2. This was identified by combining the results of previous QTL studies assessing maize tolerance to low temperatures at the germination stage. An assessment of the results of the RIL population, CSSLs, and mQTL1 found the consistent QTL to be LtQTL1-1. It was identified in bin1.06-1.07 at a confidence interval of between 200,400,148 and 201,775,619 bp. In this interval, qRT-PCR found that relative expression of the candidate genes GRMZM2G082630 and GRMZM2G115730 were both up-regulated in low-temperature tolerant lines and down-regulated in sensitive lines (P < 0.01).

Construction of A GBS-Based High-Density Genetic Map and Flower Color-Related Loci Mapping in Grasspea (Lathyrus sativus L.).

Grasspea (Lathyrus sativus L.), a legume crop with excellent resistance to a broad array of environmental stressors, has, to this point, been poorly genetically characterized. High-density genetic linkage maps are critical for draft genome assembly, quantitative trait loci (QTLs) analysis, and gene mining. The lack of a high-density genetic linkage map has limited both genomic studies and selective breeding in grasspea. Here, we developed a high-density genetic linkage map of grasspea using genotyping-by-sequencing (GBS) to sequence 154 grasspea plants, comprising 2 parents and 152 F2 progeny. In all, 307.74 Gb of data was produced, including 2,108,910,938 paired-end reads, as well as 3536 SNPs mapped to seven linkage groups (LG1–LG7). With an average length of 996.52 cM per LG, the overall genetic distance was 6975.68 cM. Both the χ2 test and QTL analysis, based on the Kruskal–Wallis (KW) test and interval mapping (IM) analysis, revealed the monogenic inheritance of flower color in grasspea, with the responsible QTL located between 308.437 cM and 311.346 cM in LG4. The results can aid grasspea genome assembly and accelerate the selective breeding of new grasspea germplasm resources.

A high-density genetic linkage map and QTL mapping for sex in Clarias fuscus

Hong Kong catfish (Clarias fuscus) is a freshwater fish that has economic value and is widely cultured in southern China. C. fuscus has significant sexual growth dimorphism. In this study, full-sib F1 individuals of C. fuscus were used as a mapping family to construct a high-density genetic linkage map, and sex-related quantitative trait loci (QTL) were mapped using single nucleotide polymorphism (SNP) markers by restriction-site associated DNA sequencing (RAD-seq) technology. The genetic map was divided into 28 linkage groups with a total map distance of 4870.15 cM, 6453 markers, and an average genetic distance of 0.75 cM between markers. Based on the genetic linkage map, interval mapping was performed to identify sex-related QTLs. A sex-related QTL, qSEX-1, was successfully mapped to LG13, which contained 225 linked SNP markers. The LOD value for the main QTL peak was 77.18, located at 138.32 cM, and the proportion of phenotypic variance explained (PVE) for sex was 83.1%. A candidate sex-determination region was identified within the qSEX-1 interval, with a total map distance of 16.073 cM and 15 SNP markers. The np544 marker was highly linked to sex. In summary, the first genetic linkage map of C. fuscus was generated based on high-throughput sequencing. Moreover, sex-linked SNP loci and a sex-determining interval were identified, providing methodological guidance and important tools for sex control technology in C. fuscus breeding.

Construction of a high-density genetic linkage map and QTL mapping for growth traits in gynogenetic brown-marbled grouper (Epinephelus fuscoguttatus)

High-density genetic linkage maps based on single nucleotide polymorphisms (SNPs) are essential for quantitative trait loci (QTL) mapping, trait-related gene identification, marker-assisted selection (MAS), genome assembly, and comparative genomic analysis in aquaculture fish species. Haploid (or gynogenesis) is an excellent germplasm target for mapping genetic linkage maps and MAS breeding. In this study, the high-density genetic linkage map of gynogenetic brown-marbled grouper (Epinephelus fuscoguttatus) based on genotyping by sequencing (GBS) technology was constructed using one F1 gynogenetic family composed of 164 gynogens and their female parents. A high-density linkage map of gynogenetic brown-marbled grouper was constructed with 19,301 SNPs located in 24 linkage groups (LGs). The genetic length of the consensus map was 2343.72 cM, with an average genetic length of 97.655 cM and an average marker interval of 0.12 cM. QTL mapping analysis revealed forty QTLs for body mass and ten phenotypic traits in 9 LGs. Multiple loci were found to be shared on LG3, LG8, LG11, LG16 and LG23, and several important growth-related candidate genes (e.g., mrc1, adgrb3, zbtb38 and adcy3), were identified within QTL regions. These vital SNPs and candidate genes may serve as useful genomic tools for marker-assisted selective breeding. Coupled breeding of MAS and artificial gynogenesis could provide a powerful method for genetic improvement in grouper breeding.

Coordinate Inheritance of Seed Isoflavone and Protein in Soybean

Soybean (Glycine max (L.) Merr.) is an important nutritional crop, not only as a rich source of protein and oil, but also for the production of isoflavones. There is a demand to breed soybean cultivars bearing consistently high protein, oil and isoflavone yields, yet this requires a clear heritable genetic relationship among isoflavone, protein and oil production. Here, two soybean genotypes contrasting in terms of protein, oil and isoflavone contents and their 185 F8:10 recombinant inbred lines (RILs) were employed to characterize seed protein, oil and isoflavone contents over two years of field trials. In this population, protein, but not oil, was significantly correlated with isoflavone content. A high-density genetic linkage map containing 3943 SNP markers identified through genotyping-by-sequencing (GBS) technology was constructed for further genetic analysis, whereby a total of 25 integrated isoflavone loci were identified, including qISO1, qISO 6.1, qISO 6.3 and qISO 6.4, which are newly identified QTLs. Two major QTLs identified in this study, qISO5 and qISO6.2, were fine-mapped for production of daidzein and genistein derivatives, as well as for glycitein derivatives, in the sequences between nucleotide positions 41042159 and 42098680 on chromosome 5 and between 18449510 and 19395795 on chromosome 6, which, respectively, explain 9.3–20.4% and 7.8–24.8% of the phenotypic variation in these traits. Further combination of qISO5 and qISO6.2 resulted in additive impacts on isoflavone production. Among the 13 QTLs linked with seed protein content in this study, three also colocated with QTLs for isoflavone content, indicating that seed isoflavone and protein content may be coordinately inherited. These results contribute to understanding the relationships between isoflavone and protein or oil content in soybean seeds. This knowledge could be valuable for soybean breeding programs aiming to combine consistently high isoflavone production with high protein or oil content.

Construction of a high-density genetic linkage map and QTL mapping of growth and cold tolerance traits in tiger puffer Takifugu rubripes

The tiger puffer (Takifugu rubripes) is an important aquaculture species, and its low temperature tolerance breeding has a positive impact on the industry. However, genetic improvement of the species is still in its infancy. In order to promote the breeding process of tiger puffer, the construction of a genetic linkage map and the identification and validation of molecular markers associated with traits are the first steps towards marker-assisted selection (MAS). In this study, a high-density genetic linkage map of the tiger puffer was constructed by whole-genome resequencing. The map consisted of 4416 bin markers distributed over 22 linkage groups (LGs) with a total genetic coverage of 3147.8 cM and an average density of 0.76 cM. On this basis, quantitative trait locus (QTL) mapping results revealed that 14 QTLs associated with body weight, body length and total length were identified in five LGs at the genome-wide significance threshold, explaining 11.1–16.7% of the phenotypic variation. Among them, 10 QTLs were located in LG3, with the QTLs associated with body weight all located in LG3. There were four QTLs with overlapping regions which were associated with both body weight and total length. In addition, this study completed the QTL analysis of cold resistance traits of tiger puffer for the first time, and the results showed that eight QTLs were identified in six LGs, which explained 13.6–16.3% of the phenotypic variation. The linkage map and QTL for important economic traits obtained in this study provide useful tools for genetic research and molecular marker-assisted breeding of tiger puffer.

Corrigendum to: Identification of salt tolerance QTL in a wheat RIL mapping population using destructive and non-destructive phenotyping.

Bread wheat (Triticum aestivum L.) is one of the most important food crops, however it is only moderately tolerant to salinity stress. To improve wheat yield under saline conditions, breeding for improved salinity tolerance of wheat is needed. We have identified nine quantitative trail loci (QTL) for different salt tolerance sub-traits in a recombinant inbred line (RIL) population, derived from the bi-parental cross of Excalibur × Kukri. This population was screened for salinity tolerance subtraits using a combination of both destructive and non-destructive phenotyping. Genotyping by sequencing (GBS) was used to construct a high-density genetic linkage map, consisting of 3236 markers, and utilised for mapping QTL. Of the nine mapped QTL, six were detected under salt stress, including QTL for maintenance of shoot growth under salinity (QG ( 1-5 ) .asl -5A , QG ( 1-5 ) .asl -7B ) sodium accumulation (QNa.asl -2A ), chloride accumulation (QCl.asl -2A , QCl.asl -3A ) and potassium : sodium ratio (QK :Na.asl -2DS2 ). Potential candidate genes within these QTL intervals were shortlisted using bioinformatics tools. These findings are expected to facilitate the breeding of new salt tolerant wheat cultivars. Soil salinity causes major yield losses in bread wheat, which is moderately tolerant to salinity stress. Using high throughput genotyping and phenotyping techniques, we identified quantitative trail loci (QTL) for different salt tolerance sub-traits in bread wheat and shortlisted potential candidate genes. These QTL and candidate genes may prove useful in breeding for salt tolerant wheat cultivars.