Miscanthus is a perennial rhizomatous grass belonging to Andropogoneae, which is now used as lignocellulosic biomass crop. Miscanthus has a short history of domestication, so further breeding effort ...for improved biomass production is needed. Flowering plays a critical role in controlling vegetative growth and physiology of plant, so this study focused on finding quantitative trait locus controlling flowering of Miscanthus for use in marker assisted breeding. A cross-pollinated M. sinensis F1 population consisted of 278 progenies was produced, transplanted to the field and assessed in their flowering traits. Julian dates of flag leaf extension, first heading, half heading, first flowering, and half flowering were assessed in 2019, the third year after transplanting when Miscanthus was well established. The average Julian dates of the flowering traits were 198±9, 224±14, 233±14, 239±15 and 253±12, respectively, and showed a proximal normal distribution. Genotype by sequencing conducted by Illumina-hiseq using leaf DNA samples revealed the genetic map consisted of 1988 SNPs with average distance of 1.35 cM. Nine QTLs controlling flowering were detected exceeded 60% of LOD score threshold. These QTLs were neighboring 16 SNP markers, 5 of which were contained in known functional genes including RGL2 (gibberellin pathway regulation). Genetic map and marker information acquired through this study, including either annotated or not annotated markers, are expected to help understand and help breeding new Miscanthus in the future with desired flowering.
•Five flowering traits were closely related to each other.•A dense linkage map of 1988 SNPs within 2663 cM was constructed by NGS and reference mapping for Miscanthus sinensis.•Nine QTLs and neighboring 16 SNPs were discovered to control flowering traits.•One common SNP associated with 3 QTLs located at linkage group 7 newly discovered was related to all five flowering traits.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Although various forms of linkage map construction software are widely available, there is a distinct lack of packages for use in the R statistical computing environment (R Core Team 2017). This ...article introduces the ASMap linkage map construction R package which contains functions that use the efficient MSTmap algorithm (Wu, Bhat, Close, and Lonardi 2008) for clustering and optimally ordering large sets of markers. Additional to the construction functions, the package also contains a suite of tools to assist in the rapid diagnosis and repair of a constructed linkage map. The package functions can also be used for post linkage map construction techniques such as fine mapping or combining maps of the same population. To showcase the efficiency and functionality of ASMap, the complete linkage map construction process is demonstrated with a high density barley backcross marker data set.
Viral Nervous Necrosis (VNN) is a major threat for the European sea bass (Dicentrarchus labrax) aquaculture industry. The improvement of disease resistance through selective breeding is a promising ...option to reduce outbreaks. With the development of high-throughput genotyping technologies, identification of genomic regions involved in the resistance could improve the efficiency of selective breeding. The aim of this study was to identify quantitative trait loci (QTL) involved in VNN resistance and to quantify their effect.
Four experimental backcross families comprising 378, 454, 291 and 211 individuals and two commercial populations A and B comprising 1027 and 1042 individuals obtained from partial factorial crosses (59♂ x 20♀ for pop A; 39♂ x 14♀ for pop B) were submitted to a redspotted grouper nervous necrosis virus (RGNNV) challenge by bath. A high-density single nucleotide polymorphism (SNP) chip panel was designed to develop the ThermoFisher Axiom™ 57k SNP DlabChip, which was used for genotyping all individuals and building a high quality linkage map. In the backcross families, composite interval mapping was performed on 30,917, 23,592, 30,656 and 31,490 markers, respectively. In the commercial populations, 40,263 markers in pop A and 41,166 markers in pop B were used to perform genome-wide association studies (GWAS) using a GBLUP and a BayesCπ approach.
One QTL was identified on chromosome LG12 in three of the four experimental backcross families, and one additional QTL on LG8 was detected in only one family. In commercial populations, QTL mapping revealed a total of seven QTLs, among which the previously mentioned QTL on LG12 was detected in both. This QTL, which was mapped to an interval of 3.45 cM, explained 9.21% of the total genetic variance in pop A, while other identified QTLs individually explained less than 1% of the total genetic variance.
The identification of QTL regions involved in VNN resistance in European sea bass, with one having a strong effect, should have a great impact on the aquaculture industry. Future work could focus on the fine mapping of the causal mutation present on LG12 using whole genome sequencing.
•Viral Nervous Necrosis is a major disease for European sea bass.•A novel SNP array for European sea bass was designed.•A total of nine QTL were detected.•One QTL, shared by five over six of the data sets and located on the LG12 explained 9.2% of the total genetic variance.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
An experiment was conducted during 2021–22 at Punjab Agricultural University, Ludhiana, Punjab for the development of linkage map and identification of QTLs for pyrenophora or Helminthosporium leaf ...spot resistance in oats (Avena sativa L.). A total of 96 F2 plants were used which was derived from the cross EC/0007662 (resistant source) and EC/0131291 (susceptible source). Linkage map was constructed for genotypic data of 96 population lines with 24 polymorphic SSR markers using QTL cartographer. A total of 7 linkage groups (LGs) had been generated from this data. But out of 7 LGs, 5 LGs remained individually at 0 position (unlinked) i.e. belonged to different group each and LG1 and LG7 were grouped. First LG included ABAM232, ABAM493 and ABAM077 from 0 to 66.5 cM. Similarly, 7th LG had two marker position i.e. ABAM342 and ABAM425. Maximum distance between the two markers was found to be 33.4 cM (between the marker interval of ABAM232 and ABAM497. Further QTL analysis was done using cartographer with composite interval mapping to identify the QTLs associated with disease resistance by comparing the phenotypic data of F2 population for disease and genotypic data of the population. The work reported here constitutes a major step toward identification of genetic regions responsible for disease resistance. However, the utility of QTL for marker assisted selection requires that QTLs are localized in a narrow region tightly linked with associated markers. The result of the experiment can be used for marker assisted breeding to transfer such genes identified as part of our research in order to reduce disease severity and yield losses in oats.
Characterization of gene family expansions and crossing over is crucial for understanding how organisms adapt to the environment. Here, we develop a high-density linkage map and detailed genome ...annotation of the painted lady butterfly (Vanessa cardui) - a non-diapausing, highly polyphagous species famous for its long-distance migratory behavior and almost cosmopolitan distribution. Our results reveal a complex interplay between regional recombination rate variation, gene duplications and transposable element activity shaping the genome structure of the painted lady. We identify several lineage specific gene family expansions. Their functions are mainly associated with protein and fat metabolism, detoxification, and defense against infection - critical processes for the painted lady’s unique life-history. Furthermore, the detailed recombination maps allow us to characterize the regional recombination landscape, data that reveal a strong effect of chromosome size on the recombination rate, a limited impact of GC-biased gene conversion and a positive association between recombination and short interspersed elements.
•Data: Gene and repeat annotations and a recombination map for Vanessa cardui.•Gene families associated with metabolism, detoxification and defense have expanded.•Chromosome size is a main determinant of the recombination rate in butterflies.•Recombination is associated with density of transposable elements.•The W-chromosome is enriched for transposable elements and lacks functional genes.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
High-density genetic linkage map based on single nucleotide polymorphisms (SNPs) are essential for fine mapping of QTLs and identification of trait-related genes in aquaculture fish species. In this ...study, the first high-density genetic linkage map of red-tail catfish (Hemibagrus wyckioides) based on 2b-RAD sequencing technology was constructed using one F1 family composed of 165 offspring and their parents. A total of 2369 SNP markers were assigned to 29 linkage groups (LGs) and the map spanned 2067.35 cM with an average SNP marker interval of 0.87 cM and genome coverage of 98.16%. QTL mapping analysis revealed that 2 significant and 15 suggestive QTLs for all four morphometric traits were identified on 10 LGs, explaining 7.4–13.3% of phenotypic variations. Some candidate growth-related genes such as ttc39b, lrp1, gng3, aspp2, mgp and rusc2 were identified within QTL intervals, and a SNP in ttc39b was found to be significantly associated with body weight in different genetically unrelated populations of red-tail catfish. In addition, one genome-wide significance sex-related QTL was detected on the LG20 with a contribution to phenotypic variation of 44.2–85.7%. A total of 10 potential sex dimorphic genes, such as vps54, tsg10, pld6, psmd8 and gpa33, were also identified within or near the sex QTL markers in LG20. It suggests that the LG20 may be a sex-related LG in red-tail catfish. This high-density genetic map not only enables us to fine-map these genes related with the economic traits, but also provides effective information for future marker-assisted selection and sex-control breeding in this species.
•A first high-density genetic map with 2,369 SNPs was constructed using 2b-RAD sequencing technology.•17 growth-associated QTLs were identified and a growth-related SNP was detected in the exon 20 of candidate gene ttc39b.•One major sex-related QTL was detected on the LG20 and 10 potential sex dimorphism genes were identified within QTL regions.•This study provides valuable information for further marker-assisted selection breeding in red-tail catfish.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Multiparent advanced generation intercross (MAGIC) populations were recently developed to allow the high-resolution mapping of quantitative traits. We present a genetic linkage map of an elite but ...highly diverse eight-founder MAGIC population in common wheat (
L.). Our MAGIC population is composed of 394 F
recombinant inbred lines lacking significant signatures of population structure. The linkage map included 5435 SNP markers distributed over 2804 loci and spanning 5230 cM. The analysis of population parameters, including genetic structure, kinship, founder probabilities, and linkage disequilibrium and congruency to other maps indicated appropriate construction of both the population and the genetic map. It was shown that eight-founder MAGIC populations exhibit a greater number of loci and higher recombination rates, especially in the pericentromeric regions, compared to four-founder MAGIC, and biparental populations. In addition, our greatly simplified eight-parental MAGIC mating design with an additional eight-way intercross step was found to be equivalent to a MAGIC design with all 210 possible four-way crosses regarding the levels of missing founder assignments and the number of recombination events. Furthermore, the MAGIC population captured 71.7% of the allelic diversity available in the German wheat breeding gene pool. As a proof of principle, we demonstrated the application of the resource for quantitative trait loci mapping analyzing seedling resistance to powdery mildew. As wheat is a crop with many breeding objectives, this resource will allow scientists and breeders to carry out genetic studies for a wide range of breeder-relevant parameters in a single genetic background and reveal possible interactions between traits of economic importance.
Growth related traits controlled by quantitative trait loci (QTL) are important economic traits in aquaculture fish species. In order to dissect these QTL, a high-density genetic linkage map is ...particularly important. In this study, the first high-density genetic linkage map of black carp (Mylopharyngodon piceus) was constructed using one F1 family comprising of 128 progenies, based on genotyping-by-sequencing (GBS). A total of 10,390 single nucleotide polymorphisms (SNPs) were discovered and genotyped. A number of 4108 high-quality SNPs were assigned to 24 linkage groups (LGs) and the total length of the map was 1708.53 cM with a resolution of 0.51 cM. Conserved syntenic relationship between the high-density linkage map and the zebrafish chromosomes was detected. Relying on this high-density linkage map, 17 suggestive QTL: one for body weight, four for body length, six for body height, and six for body wide, were identified on three linkage groups (LG10, LG17, LG20). The phenotypic variance explained (PVE) by these QTL ranged from 10.9 to 15.5%. The high-density genetic linkage map serves as valuable genomic resources not only for understanding the genomic basis of economically important traits in this fish species, but also for comparative genomics and evolutionary studies of black carp. The identified QTL provide important value for ongoing marker assisted selection (MAS) in this fish.
•The first genetic linkage map for black carp with an average resolution of 0.51 cM per locus was constructed using 4197 SNPs•17 QTL related to body weight, body length, body width and body height were identified on three linkage groups•The LG1 in black carp corresponding to Chr10 and Chr22 in zebrafish genome.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Tambaqui (Colossoma macropomum) is the most important neotropical fish in freshwater aquaculture in South America. Disease outbreaks caused by the bacterium Aeromonas hydrophila have resulted in ...significant losses to tambaqui production. Selective breeding using genomic information is a powerful strategy to improve disease resistance in fish species. The first step to incorporating genomic information in breeding programs is determining the number of loci or genes that can affect targeted traits. In this study, we developed a dense linkage map for chromosome-level scaffolding and investigated the genetic architecture of resistance to A. hydrophila in tambaqui in a genome-wide association study (GWAS). The single nucleotide polymorphism (SNP) genotypes from 275 animals belonging to 18 full sib-families were obtained using the novel genotyping platform Axiom 30 K SerraSNP array for tambaqui. The genomic analysis revealed low to moderate heritability values for both resistance trait definitions: h2 = 0.26 (0.10) for test survival and h2 = 0.27 (± 0.10) for time to death. A dense linkage map was developed for tambaqui using the genotype data, resulting in 17,374 SNPs distributed across 27 linkage groups. The length of linkage groups varied from 124 (LG1) to 50 (LG14) cM, with a total integrated map length of 2298.91 cM. The female map was longer than the male map. GWAS analysis identified several putative QTLs associated with A. hydrophila resistance, distributed in six linkage groups. Several candidate genes related to immune response were located close to the putative QTLs, such as irf4a, ripk1l, il20ra, c8a, c8b, ube3c, and ccr9a. This study represents the first application of a 30 K SNP array to build a dense linkage map anchoring 27 megascaffolds (chromosomes) of the genome, and to identify genetic variants associated with A. hydrophila resistance in tambaqui.
•Development of a dense linkage map for anchoring genome scaffolds at chromosome level in tambaqui.•GWAS revealed a polygenic genetic architecture of resistance to Aeromonas hydrophila, and identified several putative QTLs.•The genes associated to significant SNPs suggest an overlap of biological systems for resistance to Aeromonas hydrophila.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Soybean is a major crop in the world and an essential source for minerals, including iron (Fe) and zin (Zn). Deficiency of Fe and Zn in soil and soybean plants result in yield loss and poor seed ...nutritional qualities. Information on genomic regions and candidate genes controlling seed Fe and Zn accumulation in soybean seed is limited. Therefore, The objective of this research was to identify genetic regions, known as quantitative trait loci (QTL), and candidate genes that control the accumulation of Fe and Zn in soybean mature seeds. A ‘Forrest’ by ‘Williams 82’ (F × W82) recombinant inbred line (RIL) population (n = 306) was used and genotyped using a total of 5405 single nucleotides polymorphism (SNP) markers using Infinium SNP6K BeadChips. A two-year experiment was conducted across two environments: North Carolina in 2018 (NC) and Illinois in 2020 (IL). Only QTL with LOD scores ≥ 2.5, as identified by the composite interval mapping (CIM) method, are reported here. In total, 6 QTL were identified for seed Fe; specifically, 3 QTL (qFe-01-NC-2018, qFe-02-NC-2018, and qFe-03-NC-2018) were located on chromosomes 1, 2, and 6, respectively, in the NC environment, and 3 QTL (qFe-01-IL-2020, qFe-02-IL-2020, and qFe-03-IL-2020) were positioned on chromosomes 1, 2, and 12, respectively, in the IL environment. A total of 6 QTL associated with seed Zn were also identified; 4 QTL (qZn-01-NC-2018; qZn-02-NC-2018; qZn-03-NC-2018; and qZn-04-NC-2018), respectively on Chr 2, 3, 7, and 19 in NC; and 2 QTL (qZn-01-IL-2020 and qZn-02-IL-2020), respectively, on Chr 5 and 8 in IL. Several functional genes encode Fe- and Zn-proteins, transcription factors, proteins-zinc finger motifs (involved in DNA binding and transcriptional regulation; crosstalk between the regulatory pathways of Zn and Fe transporters) were identified and located within the QTL interval. To our knowledge, and based on the literature available, the QTL identified here on Chr 2 and Chr 6 are novel and were not previously identified. This current research provides a new knowledge of the genetic basis of seed Fe and Zn and the markers associated with QTL. The QTL identified here will contribute to efficient marker assisted selection for higher Fe and Zn content in soybean seeds. The candidate genes and metal-responsive transcription factors may coordinate the expression of both Zn and Fe transporters in response to changes in metal availability, providing new knowledge on minerals uptake and transport mechanisms, allowing for possible genetic engineering application.
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