Analysis of Genetic Diversity for Wild Germplasm of Pleurotus pulmonarius in China Based on Whole-genome SNP Loci and Trait Characteristics

doi:10.13560/j.cnki.biotech.bull.1985.2024-0969

Abstract

Abstract:

Objective The genetic variation of the wild resources in Pleurotus pulmonarius was analyzed, aiming to provide the excellent parent strains and data support for the breeding of new varieties. Method A total of 37 wild strains were used to analyze the genetic diversity based on SNP loci obtained by whole genome resequencing, and to observe the phenotypic traits such as cultural characteristics and fruiting characteristics. Result The number of SNPs detected in the wild strains ranged from 71 521 to 114 390, and the average genetic distance between strains was 0.180. Cluster analysis showed that the closer genetic relationship among most strains from the same location, and those was closer among the strains from Shaanxi, Sichuan and Xinjiang regions in comparison with the strains from Yunnan. Abundant phenotypic diversity in culture characteristics such as favorable temperature, temperature sensitivity, colony recovery, and fruiting characteristics such as primordium formation and differentiation, fruiting body maturation, and cap color were observed in wild resources of P. pulmonarius. The cluster analysis based on phenotypic characteristics showed that all strains were divided into two groups according to primordium differentiation at the similarity coefficient of 0.52, which was highly consistent with the classification results of the principal component analysis. Conclusion The genetic variation in the wild germplasm of P. pulmonarius is abundant,which have fine potential for domestication and utilization. The degree of genetic differentiation at the genome level among wild strains might be related to their geographical distributions rather than their phenotypic characteristics.

Key words: Xiuzhengu, genetic variation, single nucleotide polymorphism, phenotypic characteristics

YUE Yuan-yuan, HU Zhe-yuan, HE Qi, HUANG Chen-yang, ZHENG Su-yue, ZHAO Meng-ran. Analysis of Genetic Diversity for Wild Germplasm of Pleurotus pulmonarius in China Based on Whole-genome SNP Loci and Trait Characteristics[J]. Biotechnology Bulletin, 2025, 41(3): 282-293.

Figures/Tables 9

References 30

1	戴玉成, 周丽伟, 杨祝良, 等. 中国食用菌名录 [J]. 菌物学报, 2010, 29(1): 1-21.
	Dai YC, Zhou LW, Yang ZL, et al. A revised checklist of edible fungi in China [J]. Mycosystema, 2010, 29(1): 1-21.
2	王祥锋, 赵威, 汪乔, 等. 10个肺形侧耳菌株的营养成分及呈味物质分析 [J]. 食品工业科技, 2023, 44(18): 352-360.
	Wang XF, Zhao W, Wang Q, et al. Analysis of nutritional and flavor components of ten strains of Pleurotus pulmonarius [J]. Sci Technol Food Ind, 2023, 44(18): 352-360.
3	中国食用菌协会. 2020年度全国食用菌统计调查结果分析 [R]. 中国食用菌, 2022, 41(1): 85-91.
	China Edible Fungi Association. Analysis of statistical survey results of edible fungi in China in 2020 [R]. Edible Fungi of China, 2022, 41(1): 85-91.
4	柯斌榕, 兰清秀, 卢政辉, 等. 秀珍菇主栽品种遗传差异及农艺性状比较 [J]. 东南园艺, 2023, 11(4): 241-247.
	Ke BR, Lan QX, Lu ZH, et al. Comparison of genetic differences and agronomic traits between the main cultivars of Pleurotus pulmonarius [J]. Southeast Hortic, 2023, 11(4): 241-247.
5	陈躬国, 林原, 刘新锐, 等. 秀珍菇遗传育种研究进展 [J]. 热带作物学报, 2017, 38(7): 1377-1381.
	Chen GG, Lin Y, Liu XR, et al. Recent advances in genetics and breeding of Pleurotus pulmonarius [J]. Chin J Trop Crops, 2017, 38(7): 1377-1381.
6	刘凌云, 周宇, 陈华, 等. 秀珍菇研究进展 [J]. 微生物学通报, 2020, 47(11): 3650-3657.
	Liu LY, Zhou Y, Chen H, et al. Research progress of Pleurotus geesteranus [J]. Microbiol China, 2020, 47(11): 3650-3657.
7	刘新锐, 叶丽云, 张黎杰, 等. 我国肺形侧耳栽培菌株交配型分析 [J]. 菌物学报, 2021, 40(12): 3109-3117.
	Liu XR, Ye LY, Zhang LJ, et al. Mating type analyses of cultivated Pleurotus pulmonarius in China [J]. Mycosystema, 2021, 40(12): 3109-3117.
8	陆娜, 王伟科, 宋吉玲, 等. 秀珍菇种质遗传多样性分析与优质菌株筛选 [J]. 中国食用菌, 2018, 37(6): 20-23.
	Lu N, Wang WK, Song JL, et al. Genetic diversity analysis and selection of high quality strains of Pleurotus geesteranus [J]. Edible Fungi China, 2018, 37(6): 20-23.
9	宋吉玲, 王伟科, 陆娜, 等. 基于农艺性状和ISSR标记的秀珍菇遗传多样性分析 [J]. 南方农业学报, 2022, 53(1): 173-181.
	Song JL, Wang WK, Lu N, et al. Genetic diversity analysis of Pleurotus pulmonarius (Fr.) Quél. based on agronomic characters and ISSR markers [J]. J South Agric, 2022, 53(1): 173-181.
10	汪乔, 王祥锋, 郭玉峰, 等. 肺形侧耳菌株的遗传差异分析与农艺性状评价 [J]. 中国农学通报, 2022, 38(10): 46-52.
	Wang Q, Wang XF, Guo YF, et al. Pleurotus pulmonarius: agronomic traits' evaluation and genetic diversity analysis [J]. Chin Agric Sci Bull, 2022, 38(10): 46-52.
11	周思琦, 龚文兵, 夏志兰, 等. 秀珍菇全基因组SSR位点分析及其在遗传多样性评估中的应用 [J]. 湖南农业大学学报: 自然科学版, 2023, 49(2): 176-182.
	Zhou SQ, Gong WB, Xia ZL, et al. Genome-wide SSR characterization and its application in evaluating the genetic diversity of Pleurotus pulmonarius [J]. J Hunan Agric Univ Nat Sci, 2023, 49(2): 176-182.
12	施肖堃, 蔡志欣, 郭仲杰, 等. 18个双孢蘑菇核心种质的重测序初步分析 [J]. 福建农业学报, 2019, 34(10): 1167-1172.
	Shi XK, Cai ZX, Guo ZJ, et al. A preliminary report on resequencing 18 representative strains of Agaricus bisporus [J]. Fujian J Agric Sci, 2019, 34(10): 1167-1172.
13	贾定洪, 王波, 何晓兰, 等. 基于基因组重测序发掘金针菇InDel、SV及丰度SNP标记 [J]. 菌物学报,2024,43(7):42-53.
	Jia DH, Wang B, He XL, et al. Exploitation of InDel, SV and abundance SNP markers in Flammulina filiformis based on genome resequencing [J]. Mycosystema, 2024, 43(7): 42-53.
14	宋琳琳, 陈红芝, 毋柳柳, 等. 基于重测序的23份香菇种质资源全基因组序列分析 [J]. 中国瓜菜, 2024, 37(3): 28-34.
	Song LL, Chen HZ, Wu LL, et al. Whole-genome squence analysis of 23 Lentinula edodes germplasms based on genome re-sequencing [J]. China Cucurbits Veg, 2024, 37(3): 28-34.
15	Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets [J]. Mol Biol Evol, 2016, 33(7): 1870-1874.
16	陈躬国, 陈剑, 吴汉琼, 等. 肺形侧耳种质资源拮抗反应及RAPD分子标记遗传多样性分析 [J]. 南方农业学报, 2020, 51(12): 2892-2900.
	Chen GG, Chen J, Wu HQ, et al. Antagonistic reaction of Pleurotus pulmonarius germplasms and genetic diversity based on RAPD molecular markers [J]. J South Agric, 2020, 51(12): 2892-2900.
17	Lu YP, Guo ZJ, Ke BR, et al. Genome-wide association study and transcriptome analysis provide candidate genes for agronomic traits of Agaricus bisporus [J]. Horticulturae, 2024, 10(7): 691.
18	林俊彬, 严俊杰, 韩星, 等. 基于全基因组重测序的杏鲍菇菌株遗传多样性与性状分析 [J]. 西南农业学报, 2023, 36(11): 2311-2318.
	Lin JB, Yan JJ, Han X, et al. Population diversity and characteristics of Pleurotus eryngii strains based on whole genome resequencing [J]. Southwest China J Agric Sci, 2023, 36(11): 2311-2318.
19	Zhao MR, Huang CY, Chen Q, et al. Genetic variability and population structure of the mushroom Pleurotus eryngii var. tuoliensis [J]. PLoS One, 2013, 8(12): e83253.
20	Xu JP, Sha T, Li YC, et al. Recombination and genetic differentiation among natural populations of the ectomycorrhizal mushroom Tricholoma matsutake from southwestern China [J]. Mol Ecol, 2008, 17(5): 1238-1247.
21	张妍, 邬向丽, 黄晨阳, 等. 金顶侧耳种质资源的遗传多样性鉴定及农艺性状评价 [J]. 北方园艺, 2018(11): 151-157.
	Zhang Y, Wu XL, Huang CY, et al. Identification of genetic diversity and evaluation of agromomic traits for the germplasm resources of Pleurotus citrinopileatus [J]. North Hortic, 2018(11): 151-157.
22	张荆城. 中国香菇群体基因组研究及主要农艺性状的全基因组关联分析 [D]. 武汉: 华中农业大学,2019.
	Zhang JC. Population genomics analysis and genome-wide association study on major agronomic traits of Lentinula edodes in China [D]. Wuhan: Huazhong Agricultural University, 2019.
23	赵梦然, 李远东, 李艳春, 等. 新疆野生阿魏蘑的IGS2-RFLP及培养特征多样性分析 [J]. 菌物学报, 2015, 34(4): 612-620.
	Zhao MR, Li YD, Li YC, et al. Genetic diversity analysis of wild Ferula mushroom based on IGS2‐RFLP markers and cultural characteristics [J]. Mycosystema, 2015, 34(4): 612-620.
24	张金霞, 赵永昌. 食用菌种质资源学 [M]. 北京: 科学出版社, 2016.
	Zhang JX, Zhao YC. Germplasm resources of edible mushroom [M]. Beijing: Science Press, 2016.
25	王雪婷, 袁菁艺, 郑苗欣, 等. 秀珍菇菌丝生物学特性研究 [J]. 农业与技术, 2022, 42(19): 12-16.
	Wang XT, Yuan JY, Zheng MX, et al. Study on biological characteristics of Pleurotus geesteranus Mycelium [J]. Agric Technol, 2022, 42(19): 12-16.
26	Larraya LM, Idareta E, Arana D, et al. Quantitative trait loci controlling vegetative growth rate in the edible basidiomycete Pleurotus ostreatus [J]. Appl Environ Microbiol, 2002, 68(3): 1109-1114.
27	林辉, 李娜娜, 李佳欢, 等. 斑玉蕈出菇产量与胞内外碳代谢的相关性分析 [J]. 菌物学报, 2022, 41(9): 1506-1518.
	Lin H, Li NN, Li JH, et al. Correlation analysis between Hypsizygus marmoreus fruiting yield and metabolism of intracellular and extracellular carbon [J]. Mycosystema, 2022, 41(9): 1506-1518.
28	沈颖越, 金群力, 蔡为明, 等. 基于重测序信息的金针菇菌株资源遗传多样性及群体结构分析 [J]. 菌物学报, 2020, 39(6): 1016-1028.
	Shen YY, Jin QL, Cai WM, et al. Analyses of population diversity and structure of Flammulina filiformis strains based on whole genome resequencing data [J]. Mycosystema, 2020, 39(6): 1016-1028.
29	努尔孜亚·亚力买买提, 贾文捷, 郝敬喆, 等. 野生平菇菌株的培养特征及遗传多样性分析 [J]. 新疆农业科学, 2021, 58(1): 143-150.
	YLMMT Nurziya, Jia WJ, Hao JZ, et al. Analysis of culture characteristics and genetic diversity of wild Pleurotus ostreatus strains [J]. Xinjiang Agric Sci, 2021, 58(1): 143-150.
30	潘春磊, 王延锋, 盛春鸽, 等. 黑木耳59个菌株的遗传多样性分析 [J]. 中国食用菌, 2022, 41(1): 17-22.
	Pan CL, Wang YF, Sheng CG, et al. Analysis on genetic differences of 59 strains of Auricularia heimuer [J]. Edible Fungi China, 2022, 41(1): 17-22.

地理来源 Origin	菌株编号（CCMSSC） Strain No.（CCMSSC）
陕西省西安市周至县	04110，04115，04112，04114，04116
四川省阿坝藏族羌族自治州	04122，04123
新疆维吾尔自治区	04930，04936，04964
云南省怒江傈僳族自治州兰坪县	04037，04040，04041
云南省迪庆藏族自治州维西县	05784，05799，05780，05795，06400，05787，05788，05789
云南省大理白族自治州剑川县	04055，05778
云南省大理白族自治州大理市	04135，04064
云南省大理白族自治州宾川县	04043，04044，04045，04046
云南省丽江市	05442
云南省楚雄彝族自治州禄丰县	04079，04080，04081
云南省红河哈尼族彝族自治州泸西县	04002
云南省西双版纳傣族自治州景洪市	04131，04132
云南省文山壮族苗族自治州麻栗坡县	04033

地理来源 Origin	菌株编号（CCMSSC） Strain No.（CCMSSC）
陕西省西安市周至县	04110，04115，04112，04114，04116
四川省阿坝藏族羌族自治州	04122，04123
新疆维吾尔自治区	04930，04936，04964
云南省怒江傈僳族自治州兰坪县	04037，04040，04041
云南省迪庆藏族自治州维西县	05784，05799，05780，05795，06400，05787，05788，05789
云南省大理白族自治州剑川县	04055，05778
云南省大理白族自治州大理市	04135，04064
云南省大理白族自治州宾川县	04043，04044，04045，04046
云南省丽江市	05442
云南省楚雄彝族自治州禄丰县	04079，04080，04081
云南省红河哈尼族彝族自治州泸西县	04002
云南省西双版纳傣族自治州景洪市	04131，04132
云南省文山壮族苗族自治州麻栗坡县	04033

菌株编号（CCMSSC） Strain No.（CCMSSC）	初始数据 Raw reads	过滤后数据 Clean reads	Q30比率 Q30/%	比对率 Mapped/%	覆盖度1X Coverage 1X/%	SNP数量 Number of SNP
04930	18 604 022	9 302 011	98.76	82.77	84.49	112 821
04936	14 811 456	7 405 728	98.82	86.20	85.49	113 207
04964	14 915 630	7 457 815	98.81	83.12	82.42	102 991
04110	18 488 524	9 244 262	98.68	85.27	86.36	114 390
04115	15 149 984	7 574 992	94.08	84.17	86.45	114 329
04112	24 353 826	12 176 913	98.71	82.65	86.68	114 021
04114	18 675 974	9 337 987	98.75	82.80	86.82	113 475
04116	14 592 300	7 296 150	98.66	85.73	85.82	113 539
04122	20 319 332	10 159 666	98.89	79.91	86.18	113 662
04123	20 756 112	10 378 056	98.46	80.18	86.31	113 841
04040	17 006 274	8 503 137	98.58	82.94	87.95	107 215
04041	19 074 448	9 537 224	98.44	84.85	86.41	105 746
04037	17 834 956	8 917 478	98.68	87.17	87.53	106 802
05784	13 651 970	6 825 985	98.58	86.35	86.32	107 036
05799	13 873 252	6 936 626	93.56	86.08	87.70	104 678
05780	14 562 546	7 281 273	98.61	84.16	80.95	78 357
05795	14 245 776	7 122 888	93.61	86.22	85.87	106 873
06400	13 632 146	6 816 073	98.07	86.59	86.17	106 642
05787	13 733 356	6 866 678	98.79	86.09	86.44	107 046
05788	15 140 038	7 570 019	98.91	83.55	85.90	105 722
05789	17 147 282	8 573 641	98.76	82.58	86.07	105 818
04064	15 755 002	7 877 501	98.76	82.80	87.12	99 371
04135	17 822 066	8 911 033	98.51	84.30	86.62	105 653
05778	20 827 486	10 413 743	98.65	82.83	85.10	87 193
04055	32 719 488	16 359 744	98.48	78.96	86.07	97 362
04043	22 664 768	11 332 384	98.88	80.82	87.61	106 967
04045	16 523 620	8 261 810	98.63	80.35	87.49	106 968
04046	16 587 060	8 293 530	98.67	83.95	87.29	106 762
04044	14 173 798	7 086 899	98.58	82.19	86.94	106 860
04081	22 760 284	11 380 142	98.65	87.00	86.02	93 862
04079	16 544 362	8 272 181	98.72	86.88	87.29	94 151
04080	17 422 988	8 711 494	98.69	86.98	84.83	93 630
04131	19 619 758	9 809 879	98.65	87.78	89.90	71 521
04132	20 075 700	10 037 850	98.68	86.89	89.76	71 614
04033	15 049 696	7 524 848	98.71	87.53	88.54	72 462
04002	22 159 406	11 079 703	98.91	85.85	88.08	107 651
05442	18 197 356	9 098 678	98.71	85.18	88.47	108 134
00494	14 439 742	7 219 871	93.95	96.20	99.47	44 817

菌株编号（CCMSSC） Strain No.（CCMSSC）	初始数据 Raw reads	过滤后数据 Clean reads	Q30比率 Q30/%	比对率 Mapped/%	覆盖度1X Coverage 1X/%	SNP数量 Number of SNP
04930	18 604 022	9 302 011	98.76	82.77	84.49	112 821
04936	14 811 456	7 405 728	98.82	86.20	85.49	113 207
04964	14 915 630	7 457 815	98.81	83.12	82.42	102 991
04110	18 488 524	9 244 262	98.68	85.27	86.36	114 390
04115	15 149 984	7 574 992	94.08	84.17	86.45	114 329
04112	24 353 826	12 176 913	98.71	82.65	86.68	114 021
04114	18 675 974	9 337 987	98.75	82.80	86.82	113 475
04116	14 592 300	7 296 150	98.66	85.73	85.82	113 539
04122	20 319 332	10 159 666	98.89	79.91	86.18	113 662
04123	20 756 112	10 378 056	98.46	80.18	86.31	113 841
04040	17 006 274	8 503 137	98.58	82.94	87.95	107 215
04041	19 074 448	9 537 224	98.44	84.85	86.41	105 746
04037	17 834 956	8 917 478	98.68	87.17	87.53	106 802
05784	13 651 970	6 825 985	98.58	86.35	86.32	107 036
05799	13 873 252	6 936 626	93.56	86.08	87.70	104 678
05780	14 562 546	7 281 273	98.61	84.16	80.95	78 357
05795	14 245 776	7 122 888	93.61	86.22	85.87	106 873
06400	13 632 146	6 816 073	98.07	86.59	86.17	106 642
05787	13 733 356	6 866 678	98.79	86.09	86.44	107 046
05788	15 140 038	7 570 019	98.91	83.55	85.90	105 722
05789	17 147 282	8 573 641	98.76	82.58	86.07	105 818
04064	15 755 002	7 877 501	98.76	82.80	87.12	99 371
04135	17 822 066	8 911 033	98.51	84.30	86.62	105 653
05778	20 827 486	10 413 743	98.65	82.83	85.10	87 193
04055	32 719 488	16 359 744	98.48	78.96	86.07	97 362
04043	22 664 768	11 332 384	98.88	80.82	87.61	106 967
04045	16 523 620	8 261 810	98.63	80.35	87.49	106 968
04046	16 587 060	8 293 530	98.67	83.95	87.29	106 762
04044	14 173 798	7 086 899	98.58	82.19	86.94	106 860
04081	22 760 284	11 380 142	98.65	87.00	86.02	93 862
04079	16 544 362	8 272 181	98.72	86.88	87.29	94 151
04080	17 422 988	8 711 494	98.69	86.98	84.83	93 630
04131	19 619 758	9 809 879	98.65	87.78	89.90	71 521
04132	20 075 700	10 037 850	98.68	86.89	89.76	71 614
04033	15 049 696	7 524 848	98.71	87.53	88.54	72 462
04002	22 159 406	11 079 703	98.91	85.85	88.08	107 651
05442	18 197 356	9 098 678	98.71	85.18	88.47	108 134
00494	14 439 742	7 219 871	93.95	96.20	99.47	44 817

菌株编号（CCMSSC） Strain No.（CCMSSC）	菌丝满瓶 Completion of spawn running	原基形成 Primordium formation	原基分化 Primordium differentiation	子实体成熟 Maturation of fruiting body	菌盖颜色 Colour of pileus
04930	能	能	能	能	浅棕
04064	能	能	能	能	浅棕
04079	能	能	能	能	浅棕
04080	能	能	能	能	浅棕
05788	能	能	能	能	深棕
05787	能	能	能	能	深棕
04002	能	能	能	能	深棕
04135	能	能	能	能	浅棕
04131	能	能	能	能	浅棕
04132	能	能	能	能	浅棕
04936	能	能	能	能	深棕
00494	能	能	能	能	深棕
04115	能	能	能	能	深棕
05789	能	能	能	能	深棕
04043	能	能	能	否	深棕
04046	能	能	能	否	深棕
04033	能	能	能	否	浅棕
04964	能	能	否	否	——
04044	能	能	否	否	——
04110	能	能	否	否	——
04045	能	能	否	否	——
04116	能	能	否	否	——
05784	能	能	否	否	——
05799	能	能	否	否	——
04037	能	能	否	否	——
06400	能	能	否	否	——
04081	能	能	否	否	——
05778	能	能	否	否	——
04055	能	能	否	否	——
04112	能	否	否	否	——
04114	能	否	否	否	——
04122	能	否	否	否	——
04041	能	否	否	否	——
05442	能	否	否	否	——
04123	能	否	否	否	——
05780	能	否	否	否	——
05795	能	否	否	否	——
04040	否	否	否	否	——