Locus Mapping Research Articles

Fine-mapping and candidate gene analysis of tuber eye depth in potato

Eye depth is an important agronomic trait affecting tubers' appearance, quality, and processing suitability. Hence, cultivating varieties with uniform shapes and shallow eye depth are important goals for potato breeding. In this study, based on the primary mapping of the tuber eye-depth locus using a small primary-segregating population, a large secondary-segregating population with 2,100 individuals was used to map the eye-depth locus further. A major quantitative trait locus for eye-depth on chromosome 10 was identified (designated qEyd10.1) using BSA-seq and traditional QTL mapping method. The qEyd10.1 could explain 55.0% of the eye depth phenotypic variation and was further narrowed to a 309.10 kb interval using recombinant analysis. To predict candidate genes, tissue sectioning and RNA-seq of the specific tuber tissues were performed. Genes encoding members of the peroxidase superfamily with likely roles in indole acetic acid regulation were considered the most promising candidates. These results will facilitate marker-assisted selection for the shallow-eye trait in potato breeding and provide a solid basis for eye-depth gene cloning and the analysis of tuber eye-depth regulatory mechanisms.

Identification of Key Genes and Pathways for Anaerobic Germination Tolerance in Rice Using Weighted Gene Co-Expression Network Analysis (WGCNA) in Association with Quantitative Trait Locus (QTL) Mapping

BackgroundRice is one of the most important food crops in the world, and with the development of direct seeding methods for rice, exposure to anaerobic stress has become a major factor limiting its growth.ResultsIn this experiment, we tested the tolerance to anaerobic germination of rice varieties NIP and HD84, and they were used as parents to construct a DH (doubled-haploid) population. The transcriptomes of NIP (highly tolerant) and HD86 (intolerant), and their progeny HR (highly tolerant) and NHR (intolerant) were sequenced from normal and anaerobic environments. The differentially-expressed genes (DEGs) were subjected to GO (Gene ontology), KEGG (Kyoto Encyclopedia of Genes and Genomes), and WGCNA analyses. QTL mapping of the DH population identified tolerance to anaerobic germination-related chromosomal segments. The transcriptome results from 24 samples were combined with the anaerobic stress QTL results for 159 DH population lines to construct a metabolic network to identify key pathways and a gene interaction network to study the key genes. Essential genes were initially subjected to rigorous functional validation, followed by a comprehensive analysis aimed at elucidating their potential utility in domestication and breeding practices, particularly focusing on the exploitation of dominant haplotypes.ConclusionThe results show that pyruvate decarboxylase (PDC) and alcohol dehydrogenase (ADH) are the starting signals of energy metabolism for coleoptile length growth, the auxin transporter EXPA is the determining signal for coleoptile length growth. The pivotal genes Os05g0498700 and Os01g0866100 exert a negative regulatory influence on coleoptile length, ultimately enhancing tolerance to anaerobic germination in rice. Analyses of breeding potential underscore the additional value of Os05g0498700-hyp2 and Os01g0866100-hyp2, highlighting their potential utility in further improving rice through breeding programs. The results of our study will provide a theoretical basis for breeding anaerobic-tolerant rice varieties.

Genetic mapping of loci affecting seedling and adult-plant resistance to powdery mildew derived from two CIMMYT wheat lines

Main conclusionPM3 and PM8 alleles carried by two CIMMYT wheat lines confer powdery mildew resistance in seedlings and/or adult plants. A stage-specific epistatic interaction was observed between PM3 and PM8.Powdery mildew is an important foliar disease of wheat. Major genes for resistance, which have been widely used in wheat breeding programs, are typically effective against only limited numbers of virulence genes of the pathogen. The main aim of this study was to map resistance loci in wheat lines 7HRWSN58 and ZWW09-149 from the International Maize and Wheat Improvement Center (CIMMYT). Doubled haploid populations (Magenta/7HRWSN58 and Emu Rock/ZWW09-149) were developed and grown in controlled environment experiments and inoculated with a composite of Blumeria graminis f.sp. tritici isolates that had been collected at various locations in Western Australia. Plants were assessed for powdery mildew symptoms (percentage leaf area diseased) on seedlings and adult plants. Populations were subjected to genotyping-by-sequencing and assayed for known SNPs in the resistance gene PM3. Linkage maps were constructed, and markers were anchored to the wheat reference genome sequence. In both populations, there were asymptomatic lines that exhibited no symptoms. Among symptomatic lines, disease severity varied widely. In the Magenta/7HRWSN58 population, most of the observed variation was attributed to the PM3 region of chromosome 1A, with the allele from 7HRWSN58 conferring resistance in seedlings and adult plants. In the Emu Rock/ZWW09-149 population, two interacting quantitative trait loci were mapped: one at PM3 and the other on chromosome 1B. The Emu Rock/ZWW09-149 population was confirmed to segregate for a 1BL·1RS translocation that carries the PM8 powdery mildew resistance gene from rye. Consistent with previous reports that PM8-derived resistance can be suppressed by PM3 alleles, the observed interaction between the quantitative trait loci on chromosomes 1A and 1B indicated that the PM3 allele carried by ZWW09-149 suppresses PM8-derived resistance from ZWW09-149, but only at the seedling stage. In adult plants, the PM8 region conferred resistance regardless of the PM3 genotype. The resistance sources and molecular markers that were investigated here could be useful in wheat breeding.

Genetic progress in cowpea [Vigna unguiculata (L.) Walp.] stemming from breeding modernization efforts at the International Institute of Tropical Agriculture.

Genetic gain has been proposed as a quantifiable key performance indicator that can be used to monitor breeding programs' effectiveness. The cowpea breeding program at the International Institute of Tropical Agriculture (IITA) has developed and released improved varieties in 70 countries globally. To quantify the genetic changes to grain yield and related traits, we exploited IITA cowpea historical multi-environment trials (METs) advanced yield trial (AYT) data from 2010 to 2022. The genetic gain assessment targeted short duration (SD), medium duration (MD), and late duration (LD) breeding pipelines. A linear mixed model was used to calculate the best linear unbiased estimates (BLUE). Regressed BLUE of grain yield by year of genotype origin depicted realized genetic gain of 22.75 kg/ha/year (2.65%), 7.91 kg/ha/year (0.85%), and 22.82 kg/ha/year (2.51%) for SD, MD, and LD, respectively. No significant gain was realized in 100-seed weight (Hsdwt). We predicted, based on 2022 MET data, that recycling the best genotypes at AYT stage would result in grain yield gain of 37.28 kg/ha/year (SD), 28.00 kg/ha/year (MD), and 34.85 kg/ha/year (LD), and Hsdwt gain of 0.48g/year (SD), 0.68g/year (MD), and 0.55g/year (LD). These results demonstrated a positive genetic gain trend for cowpea, indicating that a yield plateau has not yet been reached and that accelerated gain is expected with the recent integration of genomics in the breeding program. Advances in genomics include the development of the reference genome, genotyping platforms, quantitative trait loci mapping of key traits, and active implementation of molecular breeding.

Dissecting root system architecture traits in durum wheat–goatgrass (Triticum durum–Aegilops speltoides) backcross introgression lines

AbstractA well‐developed root system is essential for efficient nutrient and water uptake. We phenotyped a set of 172 Triticum durum–Aegilops speltoides backcross introgression lines (BILs) for various root architecture traits during 2019–2020 and 2020–2021 cropping seasons. The roots were sampled at the maximum tillering stage, and data on various root architecture traits were recorded. The quantitative trait loci (QTL) mapping was carried out using 5672 polymorphic SNPs obtained from genotyping‐by‐sequencing. A total of 21 QTLs were detected for various root architecture traits on chromosomes 1A, 2A, 2B, 3B, 5A and 6B. Stable QTLs were detected for total root length, number of root tips and root dry weight over the two seasons. Candidate genes were identified by scanning the physical interval corresponding to the linkage disequilibrium (LD) decay flanking the SNPs linked to the stable QTLs. In silico expression studies of postulated candidate genes revealed root‐specific upregulation of some of the genes. These QTLs can be used in breeding programmes after the development and validation of suitable marker assays.

Genetic Map Construction and Primary Quantitative Trait Locus Analysis of Low-Light-Stress-Related Traits in Cucumber

To ascertain the effect of low-light stress (80 μmol·m−2·s−1) on cucumbers, we report on improving and breeding low-light-tolerant varieties by mining genes related to low-light tolerance. In this study, the quantitative trait locus (QTL) mapping of cucumber plant height and internode length under low-light stress was conducted using the F2 population, employing specific-length amplified fragment sequencing (SLAF-seq) and phenotypic analysis. A genetic map with a total length of 1114.29 c M was constructed from 1,076,599 SNPs, and 2233 single-nucleotide polymorphism (SNP) markers were distributed on seven linked groups, with an average map distance of 0.50 c M. Two QTLs related to plant height, CsPlH5.1 and CsPlH6.1, were detected on Chr.5 and Chr.6, with a cumulative contribution rate of 16.33%. The contribution rate (PVE), max LOD value, additive effect (ADD), and dominant effect (DOM) of CsPlH5.1 were 9.446%, 4.013, 1.005, and 0.563, respectively. CsPlH5.1 was located between 4,812,907 and 5,159,042 in the Gy14_V2.0 genome of cucumber, with a genetic distance of 0.32 Mb; the interval contained 41 candidate genes, and CsPlH6.1 was found to be located between Marker537985 (171.10 c M) and Marker537984 (171.55 c M), a range containing only one candidate gene. A total of 42 candidate genes related to photosynthesis, chloroplast development, abiotic stress, and plant growth were found in the location range associated with plant height. Simultaneously, a QTL (Csnd2_NdL6.1) for the second internode length was detected, and the max LOD, ADD, and DOM values were 5.689, 0.384, and −0.19, respectively. Csnd2_NdL6.1 was located between 29,572,188 and 29,604,215, with 0.03 Mb on Chr.6 including seven candidate genes. The molecular function of the CsGy6G032300 gene is involved with the binding of calcium ions, which may be related to the elongation and growth of plants; however, the population needs to be further expanded for acceptable localization verification. The results of this study provide a preliminary basis for the mining of essential genes of cucumber’s low-light tolerance and identifying low-light-tolerance genes.

Evolution of a novel adrenal cell type that promotes parental care.

Cell types with specialized functions fundamentally regulate animal behaviour, and yet the genetic mechanisms that underlie the emergence of novel cell types and their consequences for behaviour are not well understood1. Here we show that the monogamous oldfield mouse (Peromyscus polionotus) has recently evolved a novel cell type in the adrenal gland that expresses the enzyme AKR1C18, which converts progesterone into 20α-hydroxyprogesterone. We then demonstrate that 20α-hydroxyprogesterone is more abundant in oldfield mice, where it induces monogamous-typical parental behaviours, than in the closely related promiscuous deer mice (Peromyscus maniculatus). Using quantitative trait locus mapping in a cross between these species, we ultimately find interspecific genetic variation that drives expression of the nuclear protein GADD45A and the glycoprotein tenascin N, which contribute to the emergence and function of this cell type in oldfield mice. Our results provide an example by which the recent evolution of a new cell type in a gland outside the brain contributes to the evolution of social behaviour.

Biofortification for Enhancement of Zinc (Zn) and Iron (Fe) Content in Wheat (Triticum aestivum L.): A Comprehensive Review

Micronutrient deficiency, often termed "hidden hunger," is a significant global health issue affecting over three billion people worldwide. Given that wheat is a primary staple grain in many developing countries, it is crucial to focus on enhancing its nutritional content, as it often lacks essential micronutrients. Biofortification offers a promising solution to this problem by increasing the levels of key nutrients in the edible parts of crops through both agronomic and genetic approaches. This article examines the potential of biofortification in wheat, targeting vital micronutrients like iron and zinc. By employing traditional breeding methods alongside modern genetic techniques such as genome sequencing, Quantitative Trait Locus (QTL) mapping, and Genome Wide Association Studies (GWAS), researchers aim to boost the bioavailability and concentration of these nutrients in wheat varieties. The genetic variability observed in wild wheat relatives plays a significant role in identifying traits that can enhance the nutritional profile of wheat. The benefits of biofortified wheat are numerous, especially for resource-limited consumers who rely heavily on cereal-based diets. Increased concentrations of iron and zinc in wheat could improve the health and well-being of these populations, helping to combat hidden hunger on a global scale. This review paper provides a comprehensive overview of the current state of agronomic and genetic strategies for wheat biofortification, with a specific focus on increasing zinc and iron content in wheat grains. It discusses the progress made in biofortification research and outlines the various breeding approaches and genetic tools used to enhance wheat's nutritional content. By leveraging these strategies, wheat biofortification has the potential to address micronutrient deficiencies and contribute to improved public health outcomes worldwide.

QTL Mapping and Candidate Gene Mining for Stem Diameter Using Genetic Basis of Cultivated Soybean and Wild Soybean

Soybean (Glycine max) is a vital food crop, serving as a major source of high-quality protein for human and animal consumption. Stem diameter is one of the primary determinants of the stem lodging resistance of a given plant, but there has been relatively little research to date focused on genes associated with this trait. To address this gap in the literature, 207 chromosome segment substitution lines (CSSLs) were generated in the present study through the crossing and backcrossing of the improved Suinong14 and the wild ZYD00006 soybean varieties. These CSSLs were then used for the mapping of quantitative trait loci (QTLs) associated with stem diameter in two-year field planting materials, leading to the identification of nine QTLs. Whole genome resequencing, RNA-seq, and qPCR were then used to evaluate candidate genes associated with stem diameter within these QTL intervals, ultimately leading to the selection of Glyma.04G004100 as a stem diameter-related gene. Subsequent qPCR analyses revealed that Glyma.04g004100 was upregulated in soybean plants with larger stem diameters, and haplotype analyses yielded results consistent with these stem diameter data in the population used to conduct this study. In summary, a series of QTLs associated with stem diameter were identified in the present study, resulting in the establishment of Glyma.04g004100 as a stem diameter-related gene. Together, these results offer a theoretical foundation for the future molecular-assisted breeding of lodging-resistant soybean varieties, and future functional research focused on Glyma.04g004100 may elucidate the molecular mechanisms and key signaling networks involved in soybean stem development.

Inheritance analysis of major lignan contents in Schisandra chinensis hybrid progeny

Schisandra chinensis (Turcz.) Baill. has been used in traditional Chinese medicine for more than 2000 years and is classified as a superior herb. To examine the inheritance of lignan content traits, we measured the contents of six lignan constituents in the fruit and stem of 142 individuals from the cross ‘Jinwuwei 1’ × ‘Zaohong’ for three successive years. The optimal genetic model for each trait was screened using a mixed major gene + polygene inheritance model. The lignan contents differed in degree of variation, with the annual average coefficient of variation ranging from 22.31% to 79.80% across the three years. Significant transgressive heterosis was observed for schisandrol B content both in the fruit and stem, whereas negative heterosis was detected for γ-schisandrin content both in the fruit and stem. The optimal genetic models were inconsistent among different lignans in the same organ and between different organs for the same lignan, which may be associated with specific gene expression patterns. The additive effects of the lignan contents were mostly positive, whereas the dominance effects were mainly negative. The results of this study provide a theoretical basis for quantitative trait locus mapping and marker-assisted breeding of lignan contents in S. chinensis.

Rapid Mapping of Quantitative Trait Loci for the Growth Habit in Peanuts Using Bulked Segregant Analysis

Rapid Mapping of Quantitative Trait Loci for the Growth Habit in Peanuts Using Bulked Segregant Analysis

Mapping of Leaf Rust Resistance Loci in Two Kenyan Wheats and Development of Linked Markers.

Leaf rust caused by the pathogen Puccinia triticina (Pt) is a destructive fungal disease of wheat that occurs in almost all wheat-growing areas across the globe. Genetic resistance has proven to be the best solution to mitigate the disease. Wheat breeders are continuously seeking new diversified and durable sources of resistance to use in developing new varieties. We developed recombinant inbred line (RIL) populations from two leaf rust-resistant genotypes (Kenya Kudu and AUS12568) introduced from Kenya to identify and characterize resistance to Pt and to develop markers linked closely to the resistance that was found. Our studies detected four QTL conferring adult plant resistance (APR) to leaf rust. Two of these loci are associated with known genes, Lr46 and Lr68, residing on chromosomes 1B and 7B, respectively. The remaining two, QLrKK_2B and QLrAus12568_5A, contributed by Kenya Kudu and AUS12568 respectively, are putatively new loci for Pt resistance. Both QLrKK_2B and QLrAus12568_5A were found to interact additively with Lr46 in significantly reducing the disease severity at adult plant growth stages in the field. We further developed a suite of six closely linked markers within the QLrAus12568_5A locus and four within the QLrKK_2B region. Among these, markers sunKASP_522 and sunKASP_524, flanking QLrAus12568_5A, and sunKASP_536, distal to QLrKK_2B, were identified as the most closely linked and reliable for marker-assisted selection. The markers were validated on a selection of 64 Australian wheat varieties and found to be polymorphic and robust, allowing for clear allelic discrimination. The identified new loci and linked molecular markers will enable rapid adoption by breeders in developing wheat varieties carrying diversified and durable resistance to leaf rust.

Differential QTL underlie wheat grain physical quality when measured using image‐based versus traditional laboratory methods

AbstractBackgroundThe marketing value of wheat (Triticum aestivum L.) is determined, in parts, by the grain's physical characteristics, owing to which they directly (or indirectly) influence milling performance and baking quality. These characteristics have been manually measured in the past, but now, digital image analysis (DIA) is being increasingly used to replace the slow phenotyping system. Here, we asked whether this could lead to the identification of the same or different genes when compared to the traditional phenotyping methods.ResultsWe measured grain physical quality on 142 wheat doubled haploids grown in the field over 2 years, and in using the quantitative trait locus (QTL) mapping approach we found that (1) for wheat grain weight, the use of DIA provided genetic information that mostly conformed to those obtained using the traditional phenotyping methods, with heritability estimates that were identical across both methods. Majority of the QTL detected were consistent between the traditional versus digital phenotyping methods; (2) a more complex architecture, however, arose from QTL analyses of hectoliter mass (HLM) and percentage of shriveled grains (SCR). The estimates for heritability varied by as much as 0.24 across methods and, more significantly, many of the detected QTL for both traits were method‐specific; (3) though method‐specific, identified QTL was mapped to genomic regions known to harbor genes for grain physical traits.ConclusionsThousand‐grain weight (TGW) is robust to a phenotyping method, but a different genetic system underlies HLM and SCR, when these were measured using traditional versus digital image analysis. For these traits, heritability estimates were larger when phenotyped using traditional methods relative to digital image analysis, suggesting that further refinements are required to better correlate digital image analysis with the traditional phenotyping methods.

Molecular breeding of flower load related traits in dioecious autotetraploid Actinidia arguta

Flowering plants exhibit a wide range of sexual reproduction systems, with the majority being hermaphroditic. However, some plants, such as Actinidia arguta (kiwiberry), have evolved into dioecious species with distinct female and male vines. In this study, we investigated the flower load and growth habits of female kiwiberry genotypes to identify the genetic basis of high yield with low maintenance requirements. Owing to the different selection approaches between female and male genotypes, we further extended our study to male kiwiberry genotypes. By combining both investigations, we present a novel breeding tool for dioecious crops. A population of A. arguta seedlings was phenotyped for flower load traits, in particular the proportion of non-floral shoots, proportion of floral shoots, and average number of flowers per floral shoot. Quantitative trait locus (QTL) mapping was used to analyse the genetic basis of these traits. We identified putative QTLs on chromosome 3 associated with flower-load traits. A pleiotropic effect of the male-specific region of the Y chromosome (MSY) on chromosome 3 affecting flower load-related traits between female and male vines was observed in an A. arguta breeding population. Furthermore, we utilized Genomic Best Linear Unbiased Prediction (GBLUP) to predict breeding values for the quantitative traits by leveraging genomic data. This approach allowed us to identify and select superior genotypes. Our findings contribute to the understanding of flowering and fruiting dynamics in Actinidia species, providing insights for kiwiberry breeding programs aiming to improve yield through the utilization of genomic methods and trait mapping.

Genome-wide expression quantitative trait locus analysis reveals silk-preferential gene regulatory network in maize.

Silk of maize (Zea mays L.) contains diverse metabolites with complicated structures and functions, making it a great challenge to explore the mechanisms of metabolic regulation. Genome-wide identification of silk-preferential genes and investigation of their expression regulation provide an opportunity to reveal the regulatory networks of metabolism. Here, we applied the expression quantitative trait locus (eQTL) mapping on a maize natural population to explore the regulation of gene expression in unpollinated silk of maize. We obtained 3,985 silk-preferential genes that were specifically or preferentially expressed in silk using our population. Silk-preferential genes showed more obvious expression variations compared with broadly expressed genes that were ubiquitously expressed in most tissues. We found that trans-eQTL regulation played a more important role for silk-preferential genes compared to the broadly expressed genes. The relationship between 38 transcription factors and 85 target genes, including silk-preferential genes, were detected. Finally, we constructed a transcriptional regulatory network around the silk-preferential gene Bx10, which was proposed to be associated with response to abiotic stress and biotic stress. Taken together, this study deepened our understanding of transcriptome variation in maize silk and the expression regulation of silk-preferential genes, enhancing the investigation of regulatory networks on metabolic pathways.

Identification of novel SNPs and candidate genes significantly affecting growth in grass carp (Ctenopharyngodon idella) through GWAS analysis

Grass carp (Ctenopharyngodon idella) is one of the most important cultivated fish species in the global freshwater aquaculture with fast growth, low cost of production and delicious meat. A breeding program to improve economically important growth traits in grass carp would benefit from effective molecular markers. Although a genetic linkage map of grass carp has been constructed, and quantitative trait loci (QTL) mapping and a genome-wide association study (GWAS) have been conducted, the effective number of SNP markers and genes currently available for breeding is still very limited. In this study, we conducted a GWAS based on re-sequencing of individuals to identify genomic regions and candidate genes potentially associated with various growth traits of grass carp, including body weight (BW), body length (BL) and body height (BH). A total of 4,854,366 high-quality SNPs were identified and located on 24 chromosomes. Among them, 31 SNPs were identified as being associated with growth traits, including 8 SNPs on chromosomes 1, 2, 10, 13, 14, 17 and 22 associated with BW, 21 SNPs on chromosomes 2, 4, 5, 8, 10, 13, 14, 15, 17, 23 and 24 correlated with BL, and 18 SNPs on chromosomes 2, 9, 10, 13, 14, 17, 23 and 24 related to BH. In addition, 13 of these SNPs were simultaneously associated with two or three growth traits. Within a 48 kb range upstream and downstream of these significant SNPs, 120 candidate genes were identified to be associated with the QTLs. Most of these genes were related to growth and development, fat metabolism, bone mineralization and differentiation, vascular development, and feeding regulation. Notably, the genes pwp1, cers5, chrebp, lsr, ctnnbip1, smoc2, ano6 and cckrb were specifically associated with growth, fat, bone formation and feeding. Our findings would provide a foundation for molecular marker-assisted selection, genomic selection, and functional analysis of growth traits in grass carp.

Advancements of Breeding and Genomics in Wheat (Triticum aestivum L.): Enhancing Yield and Nutritional Value for Sustainable Agriculture

Advancements in wheat breeding and genomics presently explores the genomic interventions driving focusing on quantitative trait loci (QTL) mapping, marker-assisted selection (MAS) and genomic selection (GS). QTL mapping emerges as a pivotal method for pinpointing markers linked with desirable traits, facilitating MAS. Furthermore, genomic selection (GS) holds immense potential for crop improvement. It also delves into the current landscape of MAS and explores various prospects of GS for wheat biofortification. Looking ahead, accelerated mapping studies combined with MAS and GS schemes are poised to further enhance wheat breeding efficiency. Dense molecular maps and a large set of ESTs (Expressed Sequence Tags) have enabled genome-wide identification of gene-rich and gene-poor regions, as well as QTL, including eQTL (Expression quantitative trait loci). Additionally, markers associated with major economic traits have facilitated MAS programs in some countries and enabled map-based cloning of several genes/QTL. Resources for functional genomics, such as TILLING and RNA interference (RNAi), alongside emerging approaches like epigenetics and association mapping, are further enriching wheat genomics research. In this review, we initially present cutting-edge genome-editing technologies in crop plants, with a specific focus on wheat, addressing both functional genomics and genetic enhancement. We subsequently delineate the utilization of additional technologies, including GWAS, high-throughput genotyping and phenotyping, speed breeding, and synthetic biology, within the context of wheat breeding. We assert that integrating genome editing with other molecular breeding strategies will significantly expedite the genetic enhancement of wheat, thus contributing to sustainable global production.

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.

An aldehyde dehydrogenase gene, GhALDH7B4_A06, positively regulates fiber strength in upland cotton (Gossypium hirsutum L.).

High fiber strength (FS) premium cotton has significant market demand. Consequently, enhancing FS is a major objective in breeding quality cotton. However, there is a notable lack of known functionally applicable genes that can be targeted for breeding. To address this issue, our study used specific length-amplified fragment sequencing combined with bulk segregant analysis to study FS trait in an F2 population. Subsequently, we integrated these results with previous quantitative trait locus mapping results regarding fiber quality, which used simple sequence repeat markers in F2, F2:3, and recombinant inbred line populations. We identified a stable quantitative trait locus qFSA06 associated with FS located on chromosome A06 (90.74-90.83 Mb). Within this interval, we cloned a gene, GhALDH7B4_A06, which harbored a critical mutation site in coding sequences that is distinct in the two parents of the tested cotton line. In the paternal parent Ji228, the gene is normal and referred to as GhALDH7B4_A06O; however, there is a nonsense mutation in the maternal parent Ji567 that results in premature termination of protein translation, and this gene is designated as truncated GhALDH7B4_A06S. Validation using recombinant inbred lines and gene expression analysis revealed that this mutation site is correlated with cotton FS. Virus-induced gene silencing of GhALDH7B4 in cotton caused significant decreases in FS and fiber micronaire. Conversely, GhALDH7B4_A06O overexpression in Arabidopsis boosted cell wall component contents in the stem. The findings of our study provide a candidate gene for improving cotton fiber quality through molecular breeding.