High-density Genetic Linkage Map Research Articles

Quantitative Trait Loci Mapping for Powdery Mildew Resistance in Wheat Genetic Population

Background/Objectives: Powdery mildew is a prevalent wheat disease that affects yield and quality. The characterization and fine mapping of genes associated with powdery mildew resistance can benefit marker-assisted breeding. Methods: In this study, quantitative trait loci (QTL) associated with powdery mildew were mapped using a high-density 35K DArT genetic linkage map developed from a population of double haploid lines (DHs) created by crossing “Jinmai 33 (a highly resistance line) with Yannong 19 (a highly susceptible line)”. Results: Three stable QTLs for powdery mildew were identified on chromosomes 1B, 2B, and 6A combined with the composite interval graphing method and multiple interval mapping, explaining phenotypic variations (PVE) that range from 4.98% to 13.25%. Notably, Qpm.sxn-1B and Qpm.sxn-2B were identified across three environments, with the PVE ranging from 9.37% to 13.25% and from 4.98% to 5.23%, respectively. The synergistic effects of these QTLs were contributed by the parental line “Jinmai 33”. Qpm.sxn-1B was the major stable QTL, and Qpm.sxn-2B was close to Pm51. Furthermore, Qpm.sxn-6A was identified in two environments, accounting for PVE values of 7.13% and 7.65%, respectively, with the resistance effects originating from the male parent. Remarkably, this locus has not been reported previously, indicating that Qpm.sxn-6A represents a newly dis-covered QTL governing powdery mildew genes. Conclusions: Five molecular markers available for mark-er-assisted selection were selected for tracking Qpm.sxn-1B and Qpm.sxn-2B in the program. The identification of this novel newly discovered QTL and markers reported in this study will be useful for marker-assisted selection of powdery mildew resistance.

Genetic Loci Mining and Candidate Gene Analysis for Determining Fatty Acid Composition in Rice

Fatty acid composition and its proportions are critical to the nutritional value and storage quality of rice (Oryza sativa L.) as the third major nutrient component in this staple food. This study involved crossing an indica rice variety, Huazhan (HZ), as the male parent, with a japonica variety, Nekken2, as the female parent, to produce the F1 generation. Subsequently, a population of 120 recombinant inbred lines (RILs) was developed through multiple generations of self-breeding. By utilizing a high-density molecular genetic linkage map and phenotypic data of four fatty acid components, we identified a total of 14 quantitative trait loci (QTLs) related to fatty acid composition across chromosomes 1, 3, 4, 6, 8, and 9. These included two QTLs for C14 content, three for C16:0 content, six for C18:1 content, and three for C18:2 content. Notably, the QTL qCOPT4.2 exhibited a high LOD score of 5.22. Within QTL intervals, genes such as OsACX3 and SLG affecting grain length were identified. The expression of candidate genes within these intervals was assessed and further analyzed by using quantitative real-time PCR. Genes such as LOC_Os01g15000, LOC_Os04g47120, LOC_Os04g49194, LOC_Os06g22080, LOC_Os06g23870, LOC_Os06g24704, LOC_Os06g30780, LOC_Os08g44840, and LOC_Os09g36860 were found to regulate fatty acid synthesis or metabolic pathways, potentially enhancing fatty acid content in rice. These QTLs are indispensable for breeding rice varieties with improved fatty acid profiles, offering new genetic resources for enhancing the nutritional and storage qualities of rice.

Development of a high-density genetic linkage map and identification of quantitativetrait loci (QTLs) associated with Botrytis cinerea resistance in strawberry(Fragaria × ananassa Duch.)

Development of a high-density genetic linkage map and identification of quantitativetrait loci (QTLs) associated with Botrytis cinerea resistance in strawberry(Fragaria × ananassa Duch.)

QTL Mapping-Based Identification of Visceral White-Nodules Disease Resistance Genes in Larimichthys polyactis.

Disease outbreaks in aquaculture have recently intensified. In particular, visceral white-nodules disease, caused by Pseudomonas plecoglossicida, has severely hindered the small yellow croaker (Larimichthys polyactis) aquaculture industry. However, research on this disease is limited. To address this gap, the present study employed a 100K SNP chip to genotype individuals from an F1 full-sib family, identify single nucleotide polymorphisms (SNPs), and construct a genetic linkage map for this species. A high-density genetic linkage map spanning a total length of 1395.72 cM with an average interval of 0.08 cM distributed across 24 linkage groups was obtained. Employing post-infection survival time as an indicator of disease resistance, 13 disease resistance-related quantitative trait loci (QTLs) were detected, and these regions included 169 genes. Functional enrichment analyses pinpointed 11 candidate disease resistance-related genes. RT-qPCR analysis revealed that the genes of chmp1a and arg1 are significantly differentially expressed in response to P. plecoglossicida infection in spleen and liver tissues, indicating their pivotal functions in disease resistance. In summary, in addition to successfully constructing a high-density genetic linkage map, this study reports the first QTL mapping for visceral white-nodules disease resistance. These results provide insight into the intricate molecular mechanisms underlying disease resistance in the small yellow croaker.

Identification of genetic loci for powdery mildew resistance in common wheat.

Powdery mildew (PM) poses an extreme threat to wheat yields and quality. In this study, 262 recombinant inbred lines (RILs) of Doumai and Shi 4185 cross were used to map PM resistance genes across four environments. High-density genetic linkage map of the Doumai/Shi 4185 RIL population was constructed using the wheat Illumina iSelect 90K single-nucleotide polymorphism (SNP) array. In total, four stable quantitative trait loci (QTLs) for PM resistance, QPm.caas-2AS, QPm.caas-4AS, QPm.caas-4BL, and QPm.caas-6BS, were detected and explained 5.6%-15.6% of the phenotypic variances. Doumai contributed all the resistance alleles of QPm.caas-2AS, QPm.caas-4AS, QPm.caas-4BL, and QPm.caas-6BS. Among these, QPm.caas-4AS and QPm.caas-6BS overlapped with the previously reported loci, whereas QPm.caas-2AS and QPm.caas-4BL are potentially novel. In addition, six high-confidence genes encoding the NBS-LRR-like resistance protein, disease resistance protein family, and calcium/calmodulin-dependent serine/threonine-kinase were selected as the candidate genes for PM resistance. Three kompetitive allele-specific PCR (KASP) markers, Kasp_PMR_2AS for QPm.caas-2AS, Kasp_PMR_4BL for QPm.caas-4BL, and Kasp_PMR_6BS for QPm.caas-6BS, were developed, and their genetic effects were validated in a natural population including 100 cultivars. These findings will offer valuable QTLs and available KASP markers to enhance wheat marker-assisted breeding for PM resistance.

Identification and fine mapping of a QTL-rich region for yield-and quality-related traits on chromosome 4BS in common wheat (Triticum aestivum L.).

Yield and quality are important for plant breeding. To better understand the genetic basis underlying yield- and quality-related traits in wheat (Triticum aestivum L.), we conducted the quantitative trait locus (QTL) analysis using recombinant inbred lines (RILs) and a high-density genetic linkage map with a 90K array. In this study, a total of 117 QTLs were detected for spike number per area (SNPA), thousand grain weight (TGW), grain number per spike (GNS), plant height (PH), spike length (SL), total spikelet number (TSN), spikelet density (SD), grain protein content (GPC), and grain starch content (GSC). Among these QTLs, 30 environmentally stable QTLs for yield- and quality-related traits were detected. Notably, five QTL-rich regions (Qrr) for yield-and/or quality-related traits were identified, including the QTL-rich region on chromosome 4BS (QQrr.cau-4B) for eight traits (SNPA, GNS, PH, SL, TSN, SD, GPC, and GSC). The stable QTL-rich region QQrr.cau-4B was delimited into a physical interval of approximately 2.47Mb. Based on the annotation information of the Chinese spring wheat genome v1.0 and parental re-sequencing results, the interval included twelve genes with sequence variations. Taken together, these results contribute to further understanding of the genetic basis of SNPA, GNS, PH, SL, TSN, SD, GPC, and GSC, and fine mapping of QQrr.cau-4B will be beneficial for gene cloning and marker-assisted selection in the genetic improvement of wheat varieties.

Construction of the First High-Density Genetic Linkage Map and QTL Mapping of Shikimic Acid Content in Liquidambar

High-quality genetic maps are effective tools for elucidating the genetic mechanisms of complex quantitative traits and facilitating marker-assisted breeding. Species within the genus Liquidambar (commonly called sweetgum), particularly Liquidambar styraciflua and Liquidambar formosana, are significant forest resources worldwide. These sweetgum trees have been extensively utilized in medical and cosmetic applications for centuries as they contain large amounts of valuable secondary metabolites. Among these, shikimic acid is a notable metabolite with significant pharmaceutical applications. Despite advances in conventional breeding and propagation techniques for sweetgum, the genetic basis and regulatory mechanisms of valuable traits remain largely unexplored. In this study, we constructed the first high-density genetic map for sweetgum using whole-genome resequencing (WGR) of 220 progeny individuals derived from a cross of L. styraciflua × L. formosana. The genetic map spanned a total distance of 1428.51 centimorgans (cM) with an average inter-marker distance of 0.33 cM, incorporating 4268 bin markers across 16 linkage groups. To identify the genetic loci controlling the shikimic acid content, quantitative trait locus (QTL) mapping was carried out based on the genetic map. Two QTLs located on linkage group (LG) 12 were detected, encompassing a total of 213 genes within the QTL interval. Some of these genes are closely related to secondary metabolism in plants, including YUCCA and DXS genes. This study presents the first high-quality genetic map of sweetgum and provides a preliminary QTL analysis for shikimic acid content. Our findings establish a foundational framework for the genetic improvement of sweetgum through marker-assisted breeding and offer valuable insights for further research in sweetgum genetics.

Genetics and plasticity of white leaf mark variegation in white clover (Trifolium repens L.).

Leaf variegation is common in plants and confers diverse adaptive functions. However, its genetic underpinnings remain largely unresolved; this is particularly true for variegation that arises through modified leaf tissue structure that affects light reflection. White clover is naturally polymorphic for structure-based white leaf mark variegation. It therefore provides a useful system to examine the genetic basis of this phenotype, and to assess potential costs to photosynthetic efficiency resulting from modified leaf structures. This study sought to map the loci controlling the white leaf mark in white clover and evaluate the relationship between white leaf mark, leaf thickness, and photosynthetic efficiency. We generated a high-density genetic linkage map from an F3 mapping population, employing reference genome-based SNP markers. White leaf mark was quantified through detailed phenotypic evaluations alongside leaf thickness to test how tissue thickness may affect the variegation phenotype. Quantitative trait locus (QTL) mapping was performed to characterize their genetic bases. Photosynthetic efficiency measurements were used to test for physiological trade-offs between variegation and photosynthetic output. The V locus, a major gene responsible for the white leaf mark polymorphism, was mapped to the distal end of chromosome 5, and several modifier loci were also mapped that contribute additively to variegation intensity. The presence and intensity of white leaf mark was associated with greater leaf thickness; however, increased variegation did not detectably affect photosynthetic efficiency. We have successfully mapped the major locus governing the white leaf mark in white clover, along with several modifier loci, revealing a complex basis for this structure-based variegation. The apparent absence of compromised photosynthesis in variegated leaves challenges the notion that variegation creates fitness trade-offs between photosynthetic efficiency and other adaptive functions. This finding suggests that other factors may maintain the white leaf mark polymorphism in white clover.

QTL mapping and candidate gene identification for lower temperature tolerance and growth traits using whole genome re-sequencing in Argopecten scallops

Lower temperature tolerance (LTT) and growth traits are vital to the success of overwintering scallop farming in the North China Sea. Bohai Red, a novel selected scallop strain is the main aquaculture species in this region. However, its poor LTT hinders its growth. To improve these traits, the larger Bohai Red scallop was crossed with the smaller bay scallop (A. irradians irradians) which tolerates low temperatures. The full-sib F1 hybrids and the whole-genome resequencing (WGR) method were used to construct a high-density genetic linkage map comprising 5925 single nucleotide polymorphisms (SNPs). The consensus linkage map consisted of 16 linkage groups spanning 1343.46 cM with an average distance of 0.23 cM. Based on this genetic linkage map, 42 potentially significant quantitative trait loci (QTLs) for LTT and growth were detected in eight different linkage groups (LGs) explaining 9.2–18.6% of the phenotypic variation. LG11 may regulate both LTT and growth as 20 QTLs were localized there. Eighteen candidate genes were identified, including 2 (SCARF1, SLC28A3) for LTT and 16 for the growth-related traits. To the best of our knowledge, the present work is one of the first to fine-map the LTT and growth-related QTLs in a genetic linkage map for hybrid Argopecten spp. scallops.

Construction of a high-density genetic map and QTL localization of body weight and wool production related traits in Alpine Merino sheep based on WGR

BackgroundThe Alpine Merino is a new breed of fine-wool sheep adapted to the cold and arid climate of the plateau in the world. It has been popularized in Northwest China due to its superior adaptability as well as excellent production performance. Those traits related to body weight, wool yield, and wool fiber characteristics, which are economically essential traits in Alpine Merino sheep, are controlled by QTL (Quantitative Trait Loci). Therefore, the identification of QTL and genetic markers for these key economic traits is a critical step in establishing a MAS (Marker-Assisted Selection) breeding program.ResultsIn this study, we constructed the high-density genetic linkage map of Alpine Merino sheep by sequencing 110 F1 generation individuals using WGR (Whole Genome Resequencing) technology. 14,942 SNPs (Single Nucleotide Polymorphism) were identified and genotyped. The map spanned 2,697.86 cM, with an average genetic marker interval of 1.44 cM. A total of 1,871 high-quality SNP markers were distributed across 27 linkage groups, with an average of 69 markers per LG (Linkage Group). Among them, the smallest genetic distance is 19.62 cM for LG2, while the largest is 237.19 cM for LG19. The average genetic distance between markers in LGs ranged from 0.24 cM (LG2) to 3.57 cM (LG17). The marker density in the LGs ranged from LG14 (39 markers) to LG1 (150 markers).ConclusionsThe first genetic map of Alpine Merino sheep we constructed included 14,942 SNPs, while 46 QTLs associated with body weight, wool yield and wool fiber traits were identified, laying the foundation for genetic studies and molecular marker-assisted breeding. Notably, there were QTL intervals for overlapping traits on LG4 and LG8, providing potential opportunities for multi-trait co-breeding and further theoretical support for selection and breeding of ultra-fine and meaty Alpine Merino sheep.

Genome-wide QTL and eQTL mapping reveal genes associated with growth rate trait of the Pacific white shrimp (Litopenaeus vannamei)

BackgroundGrowth rate is a crucial economic trait for farmed animals, but the genetic regulation of this trait is largely unknown in non-model organisms such as shrimp.ResultsIn this study, we performed genome-wide phenotypic quantitative trait loci (QTL) and expression quantitative trait loci (eQTL) mapping analyses to identify genes affecting the growth rate of Pacific white shrimp (Litopenaeus vannamei), which is the most commercially-farmed crustacean worldwide. We used RNA-sequencing of 268 individuals in a mapping population, and subsequently validated our findings through gene silencing and shrimp growth experiments. We constructed a high-density genetic linkage map comprising 5533 markers spanning 44 linkage groups, with a total distance of 6205.75 cM and an average marker interval of 1.12 cM. Our analyses identified 11 QTLs significantly correlated with growth rate, and 117,525 eQTLs. By integrating QTL and eQTL data, we identified a gene (metalloreductase STEAP4) highly associated with shrimp growth rate. RNA interference (RNAi) analysis and growth experiments confirmed that STEAP4 was significantly correlated with growth rate in L. vannamei.ConclusionsOur results indicate that the comprehensive analysis of QTL and eQTL can effectively identify genes involved in complex animal traits. This is important for marker-assisted selection (MAS) of animals. Our work contributes to the development of shrimp breeding and available genetic resources.

Construction of a high-density genetic map based on large-scale marker development in Coix lacryma-jobi L. using specific-locus amplified fragment sequencing (slaf-seq)

Coix lacryma-jobi L. is one of the most economically and medicinally important corns. This study constructed a high-density genetic linkage map of C. lacryma-jobi based on a cross between the parents 'Qianyi No. 2' × 'Wenyi No. 2' and their F2 progeny through high-throughput sequencing and the construction of a specific-locus amplified fragment (SLAF) library. After pre-processing, 325.49 GB of raw data containing 1628 M reads were obtained. A total of 22,944 high-quality SLAFs were identified, among which 3952 SLAFs and 3646 polymorphic markers met the requirements for the construction of a genetic linkage map. The integrated map contained 3605 high-quality SLAFs, which were grouped into ten genetic linkage groups. The total length of the map was 1620.39 cM, with an average distance of 0.45 cM and an average of 360.5 markers per linkage group. This report presents the first high-density genetic map of C. lacryma-jobi. This map was constructed using an F2 population and SLAF-seq approach, which allows the development of a large number of polymorphic markers in a short period. These results provide a platform for precise gene/quantitative trait locus (QTL) mapping, map-based gene separation, and molecular breeding in C. lacryma-jobi. They also help identify a target gene for tracking, splitting quantitative traits, and estimating the phenotypic effects of each QTL for QTL mapping. They are of great significance for improving the efficiency of discovering and utilizing excellent gene resources of C. lacryma-jobi.

Cloning and functional mechanism of the dwarf gene gba affecting stem elongation and cellulose biosynthesis in jute (Corchorus olitorius).

Plant height (PH) is an important factor affecting bast fiber yield in jute. Here, we report the mechanism of dwarfism in the 'Guangbaai' (gba) of jute. The mutant gba had shorter internode length and cell length compared to the standard cultivar 'TaiZi 4' (TZ4). Exogenous GA3 treatment indicated that gba is a GA-insensitive dwarf mutant. Quantitative trait locus (QTL) analysis of three PH-related traits via a high-density genetic linkage map according to re-seq showed that a total of 25 QTLs were identified, including 13 QTLs for PH, with phenotypic variation explained ranging from 2.42 to 74.16%. Notably, the functional mechanism of the candidate gene CoGID1a, the gibberellic acid receptor, of the major locus qPHIL5 was evaluated by transgenic analysis and virus-induced gene silencing. A dwarf phenotype-related single nucleotide mutation in CoGID1a was identified in gba, which was also unique to the dwarf phenotype of gba among 57 cultivars. Cogid1a was unable to interact with the growth-repressor DELLA even in the presence of highly accumulated gibberellins in gba. Differentially expressed genes between transcriptomes of gba and TZ4 after GA3 treatment indicated up-regulation of genes involved in gibberellin and cellulose synthesis in gba. Interestingly, it was found that up-regulation of CoMYB46, a key transcription factor in the secondary cell wall, by the highly accumulated gibberellins in gba promoted the expression of cellulose synthase genes CoCesA4 and CoCesA7. These findings provide valuable insights into fiber development affected by endogenous gibberellin accumulation in plants.

A high-density genetic linkage map and QTL identification for growth traits in dusky kob (Argyrosomus japonicus)

High-density genetic linkage maps provide a foundational genomic resource for quantitative trait locus (QTL) mapping, candidate gene localisation, and comparative genomic analysis. Data from such studies, in turn, can be incorporated into marker or genomics assisted selective breeding strategies for increased efficiency of aquaculture production. This study aimed to construct the first high-density genetic linkage map for dusky kob (Argyrosomus japonicus) a commercially important marine finfish in Asia, Australia, and South Africa. Using 2b-restriction site-associated DNA (2b-RAD) sequencing for genome-wide single nucleotide polymorphism (SNP) genotyping, in three full-sib F1 families (Family 1, n = 69 offspring; Family 2, n = 73 offspring; and Family 3, n = 70 offspring), led to the discovery and genotyping of 22,789 SNPs. Among these, 3992 quality filtered and informative SNPs were mapped to 24 linkage groups (LGs), aligning with the species' proposed haploid chromosome number. The total integrated genetic map spanned a length of 2550 cM with an average marker spacing of 0.68 cM, achieving a genome coverage of 98.61%. Male and female specific maps highlighted differential map lengths and recombination rates between the sexes, with the female map slightly longer and a lower recombination frequency than for the male. QTL analysis for growth-related traits, weight (W), standard length (sL), and Fulton's condition factor (K), identified a total of 25 QTLs of which five QTLs were found to be consistently shared across the traits. Collectively, these shared QTLs explained a substantial proportion of the phenotypic variance, accounting for between 9.30 and 19.30% of the observed variation, suggesting potential major genes for growth. These QTL regions led to the discovery of 65 potential candidate genes, including 11 genes that were specifically located within the shared QTLs. These genes were linked to essential biological processes, including metabolism, immunity, stress response, development, and vascular function. The establishment of this high-density genetic linkage map represents an important genomic resource for comprehending the genetic determinants of economically important traits in A. japonicus, with implications for advancing and optimising ongoing marker-assisted selection (MAS) initiatives in the species.

High-density bin-based genetic map reveals a 530-kb chromosome segment derived from wild peanut contributing to late leaf spot resistance.

Twenty-eight QTLs for LLS disease resistance were identified using an amphidiploid constructed mapping population, a favorable 530-kb chromosome segment derived from wild species contributes to the LLS resistance. Late leaf spot (LLS) is one of the major foliar diseases of peanut, causing serious yield loss and affecting the quality of kernel and forage. Some wild Arachis species possess higher resistance to LLS as compared with cultivated peanut; however, ploidy level differences restrict utilization of wild species. In this study, a synthetic amphidiploid (Ipadur) of wild peanuts with high LLS resistance was used to cross with Tifrunner to construct TI population. In total, 200 recombinant inbred lines were collected for whole-genome resequencing. A high-density bin-based genetic linkage map was constructed, which includes 4,809 bin markers with an average inter-bin distance of 0.43cM. The recombination across cultivated and wild species was unevenly distributed, providing a novel recombination landscape for cultivated-wild Arachis species. Using phenotyping data collected across three environments, 28 QTLs for LLS disease resistance were identified, explaining 4.35-20.42% of phenotypic variation. The major QTL located on chromosome 14, qLLS14.1, could be consistently detected in 2021 Jiyang and 2022 Henan with 20.42% and 12.12% PVE, respectively. A favorable 530-kb chromosome segment derived from Ipadur was identified in the region of qLLS14.1, in which 23 disease resistance proteins were located and six of them showed significant sequence variations between Tifrunner and Ipadur. Allelic variation analysis indicating the 530-kb segment of wild species might contribute to the disease resistance of LLS. These associate genomic regions and candidate resistance genes are of great significance for peanut breeding programs for bringing durable resistance through pyramiding such multiple LLS resistance loci into peanut cultivars.

Genomics insights into flowering and floral pattern formation: regional duplication and seasonal pattern of gene expression in Camellia

BackgroundThe formation and domestication of ornamental traits are influenced by various aspects, such as the recognition of esthetic values and cultural traditions. Camellia japonica is widely appreciated and domesticated around the world mainly due to its rich variations in ornamental traits. Ornamental camellias have a diverse range of resources, including different bud variations from Camellia spp. as well as inter- and intra- specific hybridization. Despite research on the formation of ornamental traits, a basic understanding of their genetics and genomics is still lacking.ResultsHere, we report the chromosomal-level reference genome of C. japonica through combining multiple DNA-sequencing technologies and obtain a high-density genetic linkage map of 4255 markers by sequencing 98 interspecific F1 hybrids between C. japonica and C. chekiangoleosa. We identify two whole-genome duplication events in C. japonica: one is a shared ancient γ event, and the other is revealed to be specific to genus Camellia. Based on the micro-collinearity analysis, we find large-scale segmental duplication of chromosome 8, resulting to two copies of the AGAMOUS loci, which may play a key role in the domestication of floral shapes. To explore the regulatory mechanisms of seasonal flowering, we have analyzed year-round gene expression patterns of C. japonica and C. azalea—a sister plant of continuous flowering that has been widely used for cross breeding. Through comparative analyses of gene co-expression networks and annual gene expression patterns, we show that annual expression rhythms of some important regulators of seasonal growth and development, including GIGANTEA and CONSTANS of the photoperiod pathway, have been disrupted in C. azalea. Furthermore, we reveal that the distinctive expression patterns of FLOWERING LOCUS T can be correlated with the seasonal activities of flowering and flushing. We demonstrate that the regulatory module involved in GIGANTEA, CONSTANS, and FLOWERING LOCUS T is central to achieve seasonality.ConclusionsThrough the genomic and comparative genomics characterizations of ornamental Camellia spp., we propose that duplication of chromosomal segments as well as the establishment of gene expression patterns has played a key role in the formation of ornamental traits (e.g., flower shape, flowering time). This work provides a valuable genomic platform for understanding the molecular basis of ornamental traits.

High-density genetic linkage mapping in Sitka spruce advances the integration of genomic resources in conifers.

In species with large and complex genomes such as conifers, dense linkage maps are a useful resource for supporting genome assembly and laying the genomic groundwork at the structural, populational, and functional levels. However, most of the 600+ extant conifer species still lack extensive genotyping resources, which hampers the development of high-density linkage maps. In this study, we developed a linkage map relying on 21,570 single nucleotide polymorphism (SNP) markers in Sitka spruce (Picea sitchensis [Bong.] Carr.), a long-lived conifer from western North America that is widely planted for productive forestry in the British Isles. We used a single-step mapping approach to efficiently combine RAD-seq and genotyping array SNP data for 528 individuals from 2 full-sib families. As expected for spruce taxa, the saturated map contained 12 linkages groups with a total length of 2,142 cM. The positioning of 5,414 unique gene coding sequences allowed us to compare our map with that of other Pinaceae species, which provided evidence for high levels of synteny and gene order conservation in this family. We then developed an integrated map for P. sitchensis and Picea glauca based on 27,052 markers and 11,609 gene sequences. Altogether, these 2 linkage maps, the accompanying catalog of 286,159 SNPs and the genotyping chip developed, herein, open new perspectives for a variety of fundamental and more applied research objectives, such as for the improvement of spruce genome assemblies, or for marker-assisted sustainable management of genetic resources in Sitka spruce and related species.

Genome wide linkage mapping for black point resistance in a recombinant inbred line population of Zhongmai 578 and Jimai 22

Black point, a black discoloration of the grain embryo, downgrades the grain quality and commodity grade. Identification of the underlying genetic loci can facilitate the improvement of black point resistance in wheat. Here, 262 recombinant inbred lines (RILs) from the cross of Zhongmai 578/Jimai 22 were evaluated for black point reaction in five environments. A high-density genetic linkage map of the RIL population was constructed with the wheat 50K single nucleotide polymorphism (SNP) array. Six stable QTLs for black point resistance, QBp.caas-2A, QBp.caas-2B1, QBp.caas-2B2, QBp.caas-2D, QBp.caas-3A and QBp.caas-5B were detected, explaining 2.1-28.8% of the phenotypic variances. The resistance alleles of QBp.caas-2B1 and QBp.caas-2B2 were contributed by Zhongmai 578 while the others were from Jimai 22. QBp.caas-2B2, QBp.caas-2D and QBp.caas-3A are overlapped with previously reported loci, whereas QBp.caas-2A, QBp.caas-2B1 and QBp.caas-5B are likely to be new. Five KASP markers, Kasp_2A_BP, Kasp_2B1_BP, Kasp_2B2_BP, Kasp_3A_BP and Kasp_5B_BP were validated in a natural population of 165 cultivars. The findings provide useful QTL and molecular markers for improvement of black point in wheat resistance in marker-assisted breeding.

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

Takifugu fasciatus is an aquaculture species with high economic value. In recent years, problems such as environmental pollution and inbreeding have caused a serious decline in T. fasciatus germplasm resources. In this study, a high-density genetic linkage map was constructed by whole-genome resequencing. The map consists of 4891 bin markers distributed across 22 linkage groups (LGs), with a total genetic coverage of 2381.353 cM and a mean density of 0.535 cM. Quantitative trait locus (QTL) localization analysis showed that a total of 19 QTLs associated with growth traits of T. fasciatus in the genome-wide significance threshold range, distributed on 11 LGs. In addition, 11 QTLs associated with cold tolerance traits were identified, each scattered on a different LG. Furthermore, we used QTL localization analysis to screen out three candidate genes (IGF1, IGF2, ADGRB) related to growth in T. fasciatus. Meanwhile, we screened three candidate genes (HSP90, HSP70, and HMGB1) related to T. fasciatus cold tolerance. Our study can provide a theoretical basis for the selection and breeding of cold-tolerant or fast-growing T. fasciatus.

Mapping of major QTL and candidate gene analysis for hull colour in foxtail millet (Setaria italica (L.) P. Beauv.)

BackgroundHull colour is an important morphological marker for selection in seed production of foxtail millet. However, the molecular mechanisms underlying hull colour variation remain unknown.ResultsAn F7 recombinant inbred line (RIL) population containing 215 lines derived from Hongjiugu × Yugu18 was used to analyze inheritance and detect the quantitative trait loci (QTL) for four hull colour traits using major gene plus polygene mixed inheritance analysis and composite interval mapping (CIM) in four environments. Genetic analysis revealed that the hull colour L* value (HCL*) was controlled by two major genes plus additive polygenes, the hull colour a* value (HCa*) was controlled by three major genes, the hull colour b* value (HCb*) was controlled by two major genes plus polygenes, and the hull colour C* value (HCC*) was controlled by four major genes. A high-density genetic linkage map covering 1227.383 cM of the foxtail millet genome, with an average interval of 0.879 cM between adjacent bin markers, was constructed using 1420 bin markers. Based on the genetic linkage map and the phenotypic data, a total of 39 QTL were detected for these four hull colour traits across four environments, each explaining 1.50%–49.20% of the phenotypic variation. Of these, six environmentally stable major QTL were co-localized to regions on chromosomes 1 and 9, playing a major role in hull colour. There were 556 annotated genes within the two QTL regions. Based on the functions of homologous genes in Arabidopsis and the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) gene annotations, five genes were predicted as candidate genes for further studies.ConclusionsThis is the first study to use an inheritance model and QTL mapping to determine the genetic mechanisms of hull colour trait in foxtail millet. We identified six major environmentally stable QTL and predicted five potential candidate genes to be associated with hull colour. These results advance the current understanding of the genetic mechanisms underlying hull colour traits in foxtail millet and provide additional resources for application in genomics-assisted breeding and potential isolation and functional characterization of the candidate genes.