Analysis of Population Diversity and Structure of Lentinula edodes Strains Based on Whole Genome Resequencing Data

doi:10.7668/hbnxb.20194930

Abstract

Abstract:

To investigate the genetic evolution and molecular differences of Lentinula edodes germplasm resources and their hybrid progeny,it utilized whole-genome resequencing technology and analyzed genetic diversity and population structure based on single-nucleotide polymorphism(SNP)data.It involved eight main cultivated varieties,six hybrid new varieties,and two wild strains of L.edodes.The results revealed that the SNP numbers in the wild strains Y5 and Y6 were significantly higher than those in the cultivated varieties,with 158 659 and 149 422 SNPs,respectively,and they clustered in independent branches based on genetic distance.In contrast,the cultivated varieties and their hybrid progeny exhibited similar SNP numbers and genetic relationships,with SNP counts ranging from 97 295 to 105 627 and genetic distances ranging from 0.001 2 to 0.055 3,clustering within the same branch.The branches of the cultivated varieties and their hybrid progeny could be divided into six closely related groups.These included early-maturing varieties L18 and 868,early-maturing white-faced varieties RX11,QK212,and 0912,medium-maturing firm-textured varieties 808,LX1,and 168,hybrid progeny varieties JX15 and JX3 of 808,L18,and 868,hybrid progeny varieties JXB5 and JXB15 of JX15 and JX3,and hybrid progeny varieties E14 and E36 of 0912 and JXB5.Population structure and principal component analysis revealed that L.edodes germplasm resources could be divided into four subgroups.The first class included varieties RX11,QK212,and 0912,as well as their hybrid progeny E14 and E36.The second class consisted of main cultivated varieties LX1,168,and 808,along with their hybrid derivatives JX15 and JX3,which share extremely similar genetic information or background.The third class comprised L18 and 868,along with their multiple-generation,genetically improved,high-quality hybrid strains,JXB5 and JXB15,which exist in a transitional state between cultivated varieties and wild strains,with a propensity towards the cultivated varieties.The fourth class was represented by wild strains YX5 and YX6,which are distinctly different from the cultivated strains.This study clarified the genetic differences among L.edodes strains,laying the foundation for the selection of parents and the pairing of hybrid combinations in subsequent hybrid breeding.

Key words: Lentinula edodes, Whole genome resequencing, Genetic diversity, Population structure, Single-nucleotide polymorphism

CLC Number:

YAO Lan, WANG Yanan, LIU Zhenguo, MA Hong, LIU Kunang, ZHU Yanhui, ZHANG Genwei. Analysis of Population Diversity and Structure of Lentinula edodes Strains Based on Whole Genome Resequencing Data[J]. Acta Agriculturae Boreali-Sinica, 2025, 40(S1): 1-8. doi: 10.7668/hbnxb.20194930.

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Figures/Tables 7

References 33

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菌株 Strains	来源 Origin	出菇温度/℃ Temperature	菌株特征 Characteristics of strain	其他信息 Other information
808	石家庄创新食用菌研究所	8~25	中熟优质菇主栽品种	菇形圆整肉厚
168	石家庄创新食用菌研究所	8~25	中熟优质菇主栽品种	较808稍肉厚
LX1	平泉希才菌业	8~25	中早熟优质菇主栽品种	较808早出菇
L18	石家庄创新食用菌研究所	12~25	早熟肉厚、地栽品种	低温畸形菇
868	大山姑业研究开发公司	8~22	早熟品种	广温
0912	平泉希才菌业	9~28	早熟硬质菇	早熟主栽品种
RX11	自然选育株	8~28	早熟硬质菇	似0912,但柄粗
QK212	平泉希才菌业	10~25	早熟硬质菇	似0912,但肉厚
JX15	808×868杂交子代	8~27	中早熟中大型硬质菇	菇形似808
JX3	808×L18杂交子代	8~28	中熟中大硬质菇	菇形似808和L18
JXB5	JX15×JX3杂交子代	8~28	早熟、少原基、硬质菇	菇形似808
JXB15	JX15×JX3杂交子代	8~28	早熟硬质菇,20个原基	菇形似808
E14	0912×JXB5杂交子代	8~28	早熟硬质菇	菇形似0912
E36	0912×JXB5杂交子代	8~28	早熟硬质菇	较0912肉厚
YX5	凤阳山采集	8~27	早熟原基多抗性强	子实体草帽型
YX6	凤阳山采集	7~27	早熟原基多抗性强	子实体圆伞型

菌株 Strains	来源 Origin	出菇温度/℃ Temperature	菌株特征 Characteristics of strain	其他信息 Other information
808	石家庄创新食用菌研究所	8~25	中熟优质菇主栽品种	菇形圆整肉厚
168	石家庄创新食用菌研究所	8~25	中熟优质菇主栽品种	较808稍肉厚
LX1	平泉希才菌业	8~25	中早熟优质菇主栽品种	较808早出菇
L18	石家庄创新食用菌研究所	12~25	早熟肉厚、地栽品种	低温畸形菇
868	大山姑业研究开发公司	8~22	早熟品种	广温
0912	平泉希才菌业	9~28	早熟硬质菇	早熟主栽品种
RX11	自然选育株	8~28	早熟硬质菇	似0912,但柄粗
QK212	平泉希才菌业	10~25	早熟硬质菇	似0912,但肉厚
JX15	808×868杂交子代	8~27	中早熟中大型硬质菇	菇形似808
JX3	808×L18杂交子代	8~28	中熟中大硬质菇	菇形似808和L18
JXB5	JX15×JX3杂交子代	8~28	早熟、少原基、硬质菇	菇形似808
JXB15	JX15×JX3杂交子代	8~28	早熟硬质菇,20个原基	菇形似808
E14	0912×JXB5杂交子代	8~28	早熟硬质菇	菇形似0912
E36	0912×JXB5杂交子代	8~28	早熟硬质菇	较0912肉厚
YX5	凤阳山采集	8~27	早熟原基多抗性强	子实体草帽型
YX6	凤阳山采集	7~27	早熟原基多抗性强	子实体圆伞型

菌株 Strains	初数据 Raw reads	过滤后数据 Clean reads	初数据碱基数 Raw bases	过滤后碱基数 Clean bases	Q30/%
808	29 351 998	28 173 088	4 109 841 750	3 666 835 334	89.22
168	29 665 822	28 539 966	4 167 401 356	3 729 948 195	89.50
LX1	28 365 092	27 285 262	3 986 406 095	3 592 303 099	90.11
QK212	27 216 222	26 147 028	3 815 025 395	3 414 503 276	89.50
L18	27 835 454	26 842 560	3 941 030 545	3 583 268 043	90.92
868	25 271 662	24 211 080	3 528 072 249	3 155 208 073	89.43
0912	23 930 554	22 839 612	3 317 223 910	2 933 186 439	88.42
RX11	24 479 230	23 110 500	3 351 026 724	2 990 354 391	89.24
JX3	21 772 608	20 991 778	3 066 262 850	2 765 417 891	90.19
JX15	23 228 532	22 370 494	3 254 965 921	2 894 680 329	88.93
JXB5	22 622 766	21 617 122	3 140 892 892	2 793 845 390	88.95
JXB15	21 967 006	21 147 150	3 093 520 214	2 783 923 784	89.99
E14	27 550 660	26 368 058	3 853 690 478	3 461 661 011	89.83
E36	29 474 052	28 512 444	4 177 232 954	3 779 502 043	90.48
YX5	25 677 076	24 546 928	3 582 574 942	3 253 741 423	90.82
YX6	25 345 424	24 269 438	3 539 173 032	3 154 564 489	89.13

菌株 Strains	初数据 Raw reads	过滤后数据 Clean reads	初数据碱基数 Raw bases	过滤后碱基数 Clean bases	Q30/%
808	29 351 998	28 173 088	4 109 841 750	3 666 835 334	89.22
168	29 665 822	28 539 966	4 167 401 356	3 729 948 195	89.50
LX1	28 365 092	27 285 262	3 986 406 095	3 592 303 099	90.11
QK212	27 216 222	26 147 028	3 815 025 395	3 414 503 276	89.50
L18	27 835 454	26 842 560	3 941 030 545	3 583 268 043	90.92
868	25 271 662	24 211 080	3 528 072 249	3 155 208 073	89.43
0912	23 930 554	22 839 612	3 317 223 910	2 933 186 439	88.42
RX11	24 479 230	23 110 500	3 351 026 724	2 990 354 391	89.24
JX3	21 772 608	20 991 778	3 066 262 850	2 765 417 891	90.19
JX15	23 228 532	22 370 494	3 254 965 921	2 894 680 329	88.93
JXB5	22 622 766	21 617 122	3 140 892 892	2 793 845 390	88.95
JXB15	21 967 006	21 147 150	3 093 520 214	2 783 923 784	89.99
E14	27 550 660	26 368 058	3 853 690 478	3 461 661 011	89.83
E36	29 474 052	28 512 444	4 177 232 954	3 779 502 043	90.48
YX5	25 677 076	24 546 928	3 582 574 942	3 253 741 423	90.82
YX6	25 345 424	24 269 438	3 539 173 032	3 154 564 489	89.13

菌株 Strains	GC含量/% GC content	比对率/% Mapping rate	覆盖度/% Coverage	覆盖深度 Depths	SNP总数 SNP number	InDel总数 InDel number
808	45.47	94.91	86.17	95.06	104 910	15 508
168	45.21	94.11	86.17	95.32	105 464	15 588
LX1	46.58	94.99	86.19	92.14	105 184	15 443
QK212	46.28	94.48	86.88	87.88	97 389	14 546
L18	45.54	94.90	86.59	91.01	105 627	15 614
868	44.46	95.10	86.30	81.84	104 179	15 593
0912	46.27	95.33	86.72	77.16	97 295	14 538
RX11	45.74	94.67	86.88	77.09	97 582	14 607
JX3	45.12	94.35	86.03	70.29	105 536	15 516
JX15	45.20	94.73	86.02	75.12	105 028	15 322
JXB5	41.05	94.79	85.34	72.43	101 000	14 853
JXB15	45.65	95.07	85.57	71.64	101 197	15 107
E14	45.50	94.95	85.76	89.06	95 725	13 926
E36	45.76	95.27	86.13	96.94	100 221	14 865
YX5	45.15	93.52	85.78	80.52	158 659	23 159
YX6	45.65	94.64	87.19	81.10	149 422	22 021

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