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http://dx.doi.org/10.1080/12298093.2021.2018784

SNP-Based Genetic Linkage Map and Quantitative Trait Locus Mapping Associated with the Agronomically Important Traits of Hypsizygus marmoreus  

Oh, Youn-Lee (Mushroom Science Division, National Institute of Horticultural and Herbal Science, Rural Development Administration)
Choi, In-Geol (Department of Biotechnology, College of Life Science and Biotechnology, Korea University)
Jang, Kab-Yeul (Mushroom Science Division, National Institute of Horticultural and Herbal Science, Rural Development Administration)
Kim, Min-Seek (Mushroom Science Division, National Institute of Horticultural and Herbal Science, Rural Development Administration)
Oh, Min ji (Mushroom Science Division, National Institute of Horticultural and Herbal Science, Rural Development Administration)
Im, Ji-Hoon (Mushroom Science Division, National Institute of Horticultural and Herbal Science, Rural Development Administration)
Publication Information
Mycobiology / v.49, no.6, 2021 , pp. 589-598 More about this Journal
Abstract
White strains of Hypsizygus marmoreus are more difficult to cultivate than are brown strains; therefore, new white strain breeding strategies are required. Accordingly, we constructed the genetic map of H. marmoreus with 1996 SNP markers on 11 linkage groups (LGs) spanning 1380.49 cM. Prior to analysis, 82 backcrossed strains (HM8 lines) were generated by mating between KMCC03106-31 and the progenies of the F1 hybrid (Hami-18 × KMCC03106-93). Using HM8, the first 23 quantitative trait loci (QTLs) of yield-related traits were detected with high limit of detection (LOD) scores (1.98-9.86). The length, thickness, and hardness of the stipe were colocated on LG 1. Especially, length of stipe and thickness of stipe were highly correlated given that the correlation coefficients were negative (-0.39, p value ≤ .01). And a typical biomodal distribution was observed for lightness of the pileus and the lightness of the pileus trait belonged to the LG 8, as did traits of earliness and mycelial growth in potato dextrose agar (PDA) medium. Therefore, results for color traits can be suggested that color is controlled by a multi-gene of one locus. The yield trait was highly negatively correlated with the traits for thickness of the stipe (-0.45, p value ≤ .01). Based on additive effects, the white strain was confirmed as recessive; however, traits of mycelial growth, lightness, and quality were inherited by backcrossed HM8 lines. This new genetic map, finely mapped QTLs, and the strong selection markers could be used in molecular breeding of H. marmoreus.
Keywords
Hypsizygus marmoreus; backcrossing; SNP; genetic linkage map; QTL;
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1 Callac P, Moquet F, Imbernon M, et al. Evidence for ppc1, a determinant of the pilei-pellis color of agaricus bisporus fruitbodies. Fungal Genet Biol. 1998;23(2):181-188.   DOI
2 Kong WS, You CH, Yoo YB, et al. Molecular marker related to fruitbody color of Flammulina velutipes. Mycobiology. 2004;32(1):6-10.   DOI
3 Min B, Kim S, Oh YL, et al. Whole genome sequencing of Hypsizygus marmoreus. EMBL/GenBank/DDBJ databases. 2002.
4 Cox MP, Peterson DA, Biggs PJ. SolexaQA: at-a-glance quality assessment of illumina second-generation sequencing data. Bmc Bioinformatics. 2010;11:485.   DOI
5 Foulongne-Oriol M, Rodier A, Rousseau T, et al. Quantitative trait locus mapping of yield-related components and oligogenic control of the cap color of the button mushroom, Agaricus bisporus. Appl Environ Microbiol. 2012;78(7):2422-2434.   DOI
6 Han K, Jeong HJ, Yang HB, et al. An ultra-high-density bin map facilitates high-throughput QTL mapping of horticultural traits in pepper (Capsicum annuum). DNA Res. 2016;23(2):81-91.   DOI
7 Okuda Y, Ueda J, Obatake Y, et al. Construction of a genetic linkage map based on amplified fragment length polymorphism markers and development of sequence-tagged site markers for marker-assisted selection of the sporeless trait in the oyster mushroom (Pleurotus eryngii). Appl Environ Microbiol. 2012;78(5):1496-1504.   DOI
8 Lee CY, Park JE, Lee J, et al. Development of new strains and related SCAR markers for an edible mushroom, Hypsizygus marmoreus. Appl Environ Microbiol. 2000;66:5290-5300.   DOI
9 Shah SR, Ukaegbu CI, Hamid HA, et al. Evaluation of antioxidant and antibacterial activities of the stems of flammulina velutipes and Hypsizygus tessellatus (white and brown var.) extracted with different solvents. Food Measure. 2018;12(3):1947-1961.   DOI
10 Gong WB, Li L, Zhou Y, et al. Genetic dissection of fruiting body-related traits using quantitative trait loci mapping in Lentinula edodes. Appl Microbiol Biotechnol. 2016;100(12):5437-5452.   DOI
11 Park YJ, Jung ES, Singh D, et al. Spatial (cap & stipe) metabolomic variations affect functional components between brown and white beech mushrooms. Food Res Int. 2017;102:544-552.   DOI
12 Mleczek M, Siwulski M, Rzymski P, et al. Comparison of elemental composition of mushroom Hypsizygus marmoreus originating from commercial production and experimental cultivation. Sci Hortic. 2018;236:30-35.   DOI
13 Gong W, Xie C, Zhou Y, et al. A resequencing-based ultradense genetic map of Hericium erinaceusor anchoring genome sequences and identifying genetic loci associated with monokaryon growth. Front Microbiol. 2019;10:3129.   DOI
14 Okuda Y, Murakami S, Matsumoto T. A genetic linkage map of Pleurotus pulmonarius based on AFLP markers, and localization of the gene region for the sporeless mutation. Genome. 2009;52(5):438-446.   DOI
15 Xu Y, Li P, Yang Z, et al. Genetic mapping of quantitative trait loci in crops. Crop J. 2017;5(2):175-184.   DOI
16 Foulongne-Oriol M, Spataro C, Cathalot V, et al. An expanded genetic linkage map of an intervarietal Agaricus bisporus var. bisporus x A. bisporus var. burnettii hybrid based on AFLP, SSR and CAPS markers sheds light on the recombination behaviour of the species. Fungal Genet Biol. 2010;47(3):226-236.   DOI
17 Hu KH, Chu XP. Effect of several factors on mycelia characteristics and fruiting quality and biological efficiency of Hypsizygus marmoreus. CEFA 2008;27:16-18.
18 Wang G, Chen L, Tang W, et al. Identifying a melanogenesis-related candidate gene by a high-quality genome assembly and population diversity analysis in Hypsizygus marmoreus. J Genet Genomics. 2021;8527:1673.
19 Gao W, Qu J, Zhang J, et al. A genetic linkage map of Pleurotus tuoliensis integrated with physical mapping of the de novo sequenced genome and the mating type loci. Bmc Genomics. 2018;19:18.   DOI
20 Larraya LM, P erez G, Ritter E, et al. Genetic linkage map of the edible basidiomycete Pleurotus ostreatus. Appl Environ Microbiol. 2000;66(12):5290-5300.   DOI
21 Im CK, Park YH, Hammel KE, et al. Construction of a genetic linkage map and analysis of quantitative trait loci associated with the agronomically important traits of Pleurotus eryngii. Fungal Genet Biol. 2016;92:50-64.   DOI
22 Lu LX, Yao FJ, Wang P, et al. Construction of a genetic linkage map and QTL mapping of agronomic traits in auricularia Auricula-judae. J Microbiol. 2017;55(10):792-799.   DOI
23 Li H, Handsaker B, Wysoker A, et al. The sequence alignment/map format and SAMtools. Bioinformatics. 2009;25(16):2078-2079.   DOI
24 Kim JE, Oh SK, Lee JH, et al. Genome-Wide SNP calling using next generation sequencing data in tomato. Mol Cells. 2014;37(1):36-42.   DOI
25 Jordan KW, Wang S, He F, et al. The genetic architecture of genome-wide recombination rate variation in allopolyploid wheat revealed by nested association mapping. Plant J. 2018;95(6):1039-1054.   DOI
26 Van Ooijen JW. JoinMapVR 4, software for the calculation of genetic linkage maps in experimental populations. Wageningen, Netherlands: Kyazma B.V; 2006.
27 Wang S, Basten C, Zeng Z. Windows QTL cartographer 2.5. Department of statistics. Raleigh (NC): North Carolina State University; 2007.
28 Lee SH, Kim MK, Lee MK, et al. Electrophoretic karyotyping of Hypsizygus marmoreus and evaluation of variation among its basidiospores. FEMS Microbiol Lett. 2014;359(2):209-215.   DOI
29 Sun S, Feng H, Chen Z, et al. The first genetic linkage map of Hypsizigus marmoreus based on SCAR marker. Chiang Mai J Sci. 2016;43:505-510.
30 Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009;25(14):1754-1760.   DOI
31 Gao W, Baars JJP, Maliepaard C, et al. Multi-trait QTL analysis for agronomic and quality characters of Agaricus bisporus (button mushrooms). AMB Express. 2016;6(1):67   DOI
32 Gao W, Weijn A, Baars JJP, et al. Quantitative trait locus mapping for bruising sensitivity and cap color of Agaricus bisporus (button mushrooms). Fungal Genet Biol. 2015;77:69-81.   DOI