Study on Genetic Characteristics and Taxonomic Status of Wild Chinese Chestnut Based on Genome Re-sequencing

doi:10.16420/j.issn.0513-353x.2022-0537

Acta Horticulturae Sinica ›› 2023, Vol. 50 ›› Issue (8): 1622-1636.doi: 10.16420/j.issn.0513-353x.2022-0537

• Genetic & Breeding·Germplasm Resources·Molecular Biology • Previous Articles Next Articles

Study on Genetic Characteristics and Taxonomic Status of Wild Chinese Chestnut Based on Genome Re-sequencing

NIE Xinghua, ZHANG Yu, LIU Song, YANG Jiabin, HAO Yaqiong, LIU Yang, QIN Ling^*(), XING Yu^*()

Beijing Key Laboratory for Agricultural Application and New Technique，College of Plant Science and Technology， Beijing University of Agriculture，Beijing 102206，China

Received:2023-02-16 Revised:2023-04-21 Online:2023-08-25 Published:2023-08-23
Contact: QIN Ling, XING Yu

Abstract

Abstract:

The cluster analysis of 194 chestnut resources was performed based on SSR molecular markers，and the botanical characteristics of wild chestnut resources were described and compared. Forty-six representative wild and cultivated Chinese chestnut resources were selected for re-sequencing analysis，and phylogenetic and population structure analyses were performed. The clustering results showed that wild Chinese chestnuts and cultivated Chinese chestnuts had a close genetic distance，they were mixed and no obvious division;population structure analysis also further supported that wild Chinese chestnuts and cultivated Chinese chestnuts had the consistent genetic information，revealing cultivated Chinese chestnut may be domesticated from wild Chinese chestnut in situ for a limited time. This study clarified the taxonomic status of wild chestnut，namely：wild Chinese chestnut and cultivated Chinese chestnut belong to the same species. It is clear that the habit of female flower bunching is not a characteristic of wild Chinese chestnut，and a more accurate and up-to-date boundary range of wild Chinese chestnut is proposed.

Key words: Chinese chestnut, wild resource, SSR, re-sequencing, phylogeny, population structure

NIE Xinghua, ZHANG Yu, LIU Song, YANG Jiabin, HAO Yaqiong, LIU Yang, QIN Ling, XING Yu. Study on Genetic Characteristics and Taxonomic Status of Wild Chinese Chestnut Based on Genome Re-sequencing[J]. Acta Horticulturae Sinica, 2023, 50(8): 1622-1636.

Figures/Tables 9

References 22

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Study on Genetic Characteristics and Taxonomic Status of Wild Chinese Chestnut Based on Genome Re-sequencing

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来源地 Origin	经度 Longitude	纬度 Latitude		样品编号 Sample number		品种（系）名 Cultivar（line） name	数据备注 Data note			坚果质量/g Nut weight		比对率/% Mapping rate		测序深度 Average sequencing depth	高质量SNP Number of high-quality SNPs
甘肃省陇南市康县 Kang County，Longnan， Gansu	105.6553	33.4421		w_001			AB			2.5		98.44		12.2	2 521 039
	105.6553	33.4421		w_002			A			—
	105.6553	33.4421		w_003			A			2.7
	105.6377	33.3492		w_004			A			2.9
	105.6550	33.4421		w_005			A			2.8
	105.6550	33.4421		w_006			A			2.4
	105.4849	33.3040		w_007			A			2.6
	105.4849	33.3040		w_008			A			2.4
	105.5160	33.3055		w_009			A			—
	105.5160	33.3055		w_010			A			—
	105.5160	33.3055		w_011			A			—
甘肃省陇南市徽县 Hui County，Longnan， Gansu	105.7860	33.9434		w_012			A			2.7
	105.7860	33.9434		w_013			A			2.7
	105.7860	33.9434		w_014			A			2.6
	105.8657	33.9689		w_015			A			2.9
	105.8657	33.9689		w_016			AB			—		98.37		14.1	2 985 610
	105.8657	33.9689		w_017			AB			—		98.86		12.3	2 890 954
	105.8657	33.9689		w_018			A			1.8
	105.8657	33.9689		w_019			A			2.1
	106.2906	34.0435		w_020			A			—
	106.2906	34.0435		w_021			A			—
	106.2906	34.0435		w_022			A			2.5
	106.2917	34.0422		w_023			A			2.3
	106.2917	34.0422		w_024			A			2.5
	106.2857	34.0738		w_025			A			2.5
甘肃省天水市麦积区 Maiji County，Tianshui， Gansu	106.3594	34.2713		w_026			A			1.8
	106.3594	34.2713		w_027			AB			—		97.89		42.8	3 991 653
	106.3594	34.2713		w_028			A			1.8
	106.3594	34.2713		w_029			A			2.0
	106.3594	34.2713		w_030			AB			—		98.06		12.1	4 046 634
	106.3594	34.2713		w_031			A			1.9
	106.3594	34.2713		w_032			A			1.8
湖北省十堰市房县	110.6943	31.8840		w_033			A			2.4
Fang County，Shiyan，Hubei	110.6943	31.8840		w_034			A			—
四川省绵阳市北川县	104.4137	31.9429		w_035			A			2.9
Beichuan County，Mianyang，	104.4137	31.9429		w_036			A			3.1
Sichuan	104.4137	31.9429		w_037			AB			3.2		99.28		11.9	2 037 544
	104.4137	31.9429		w_038			AB			—		99.08		13.6	2 831 778
	104.4137	31.9429		w_039			AB			—		99.09		13.1	2 092 212
	104.4137	31.9429		w_040			A			2.8
	104.4137	31.9429		w_041			A			3.0
	104.4137	31.9429		w_042			A			3.0
	104.4137	31.9429		w_043			A			—
	104.4137	31.9429		w_044			A			—
四川省广元市青川县	104.7965	32.5726		w_045			A			1.4
Qingchuan County，	104.7965	32.5726		w_046			A			0.9
Guangyuan，Sichuan	104.7324	32.5927		w_047			A			1.4
	104.7393	32.5901		w_048			A			1.3
	104.7393	32.5901		w_049			A			—
	104.7393	32.5901		w_050			A			1.5
	104.7394	32.5900		w_051			A			0.9
	104.7394	32.5900		w_052			A			1.3
	104.7394	32.5900		w_053			A			1.5
	104.7394	32.5900		w_054			A			1.5
陕西省安康市镇坪县	109.5479	31.8479		w_055			A			—
Zhenping County，Ankang， Shaanxi	109.5479	31.8479		w_056			A			—
陕西省汉中市佛坪县	107.7988	33.5425		w_057			A		—
Foping County，Hanzhong，	107.7988	33.5425		w_058			A		—
Shaanxi	107.7988	33.5425		w_059			A		—
	107.7988	33.5425		w_060			A		—
	107.7988	33.5425		w_061			A		—
陕西汉中市勉县	106.6736	33.2506		w_062			A		—
Mian County，Hanzhong，	106.6691	33.2810		w_063			A		2.1
Shaanxi	106.6691	33.2810		w_064			A		2.2
	106.6687	33.2770		w_065			A		2.2
	106.6687	33.2770		w_066			A		2.4
	106.6687	33.2770		w_067			A		—
	106.6687	33.2770		w_068			A		2.1
	106.6706	33.2702		w_069			A		1.8
	106.6706	33.2702		w_070			A		—
	106.6720	33.2479		w_071			A		2.3
陕西省汉中市略阳县	105.7995	33.3510		w_072			A		2.4
Lueyang County，Hanzhong，	105.8546	33.3475		w_073			A		0.8
Shaanxi	105.7995	33.3510		w_074			A		—
	105.8546	33.3475		w_075			A		2.3
	105.8546	33.3475		w_076			A		1.8
	105.8546	33.3475		w_077			A		—
	106.0735	33.3307		w_078			A		1.7
	106.0735	33.3307		w_079			A		2.0
	106.0735	33.3307		w_080			A		2.2
	105.7995	33.3510		w_081			A		2.1
湖北省神农架	110.1325	31.4539		w_082			AB		1.0		99.15		14.3		2 942 876
Shennongjia，Hubei	110.1325	31.4539		w_083			AB		0.9		97.95		14.3		2 565 436
	110.1325	31.4539		w_084			AB		1.5		90.24		12.9		2 846 110
	110.1325	31.4539		w_085			A		1.8
	110.1325	31.4539		w_086			A		1.7
湖北省十堰市张湾区	110.5203	32.5645		w_087			A		—
Zhangwan County，Shiyan，	110.5203	32.5645		w_088			A		—
Hubei	110.5203	32.5645		w_089			A		—
	110.5203	32.5645		w_090			AB		—		98.32		12.3		1 968 663
湖北省宜昌市兴山县	111.0166	31.5069		w_091			A		2.8
Xingshan County，Yichang，	111.0166	31.5069		w_092			A		2.8
Hubei	111.0166	31.5069		w_093			AB		2.7		93.70		12.5		1 617 206
	111.0166	31.5069		w_094			AB		3.1		97.90		13.6		1 954 846
	111.0166	31.5069		w_095			A		2.2
安徽省六安市金寨县 Jinzhai County，Lu’an， Anhui	115.8391	31.7731		w_096			AB		1.9		99.37		13.7		3 118 003
	115.8391	31.7731		w_097			A		1.9
	115.8391	31.7731		w_098			A		1.6
安徽省池州市青阳县	117.8050	30.4817		w_099			AB		1.5		97.66		13.1		3 814 588
Qingyang County，Chizhou，	117.8050	30.4817		w_100			AB		1.5		95.37		15.3		2 365 942
Anhui	117.8050	30.4817		w_101			AB		1.4		97.18		13.1		2 954 685
湖北省十堰市房县 Fang County，Shiyan， Hubei	110.6943	31.8840		w_102			AB		2.0		98.88		12.2		4 012 953
	110.6943	31.8840		w_103			AB		1.3		96.55		12.8		4 060 224
	110.6943	31.8840		w_104			A		1.4
湖南省怀化市洪江	109.7925	27.2556		w_105			A		—
Hongjiang，Huaihua，Hunan	109.7925	27.2556		w_106			A		—
湖南省衡阳市南岳区 Nanyue County，Hengyang，Hunan	112.7088	27.2734		w_107			A		—
湖南省衡阳市衡阳县	112.1808	27.1739		w_108			A		—
Hengyang County，Hengyang，	112.1808	27.1739		w_109			A		—
Hunan
湖南省浏阳市	113.8608	28.0289		w_110			A		—
Liuyang，Hunan	113.8608	28.0289		w_111			A		—
	113.8608	28.0289		w_112			A		—
湖南省湘西州永顺县 Yongshun County，Xiangxi，Hunan	111.4403	27.0358		w_113			AB	2.4			99.24		15.9		1 859 623
湖南省湘西州永顺县 Yongshun County，Xiangxi，Hunan	111.4403	27.0358		w_114			AB	2.3			98.90		13.5		1 761 528
江西省宜春市袁州区 Yuanzhou County，Yichun， Jiangxi	114.4046	27.7627		w_115			A	2.2
江西省宜春市袁州区 Yuanzhou County，Yichun， Jiangxi							A
四川省都江堰市青城山 Qingchengshan，Dujiangyan，Sichuan	103.5569	30.9408		w_116			A	2.1
	103.5569	30.9408		w_117			A	2.1
	103.5569	30.9408		w_118			A	2.6
陕西省汉中市佛坪县 Foping County，Hanzhong， Shaanxi	107.7988	33.5425		w_119			A	—
陕西省汉中市佛坪县 Foping County，Hanzhong， Shaanxi	107.7988	33.5425		w_120			A	—
陕西省安康市平利县	109.3542	32.2949		w_121			A	2.7
Pingli County，Ankang，Shaanxi	109.3542	32.2949		w_122			A	2.8
陕西省宝鸡市太白县 Taibai County，Baoji， Shaanxi	107.3165	34.0621		w_123			AB	2.8			97.57		38.4		3 090 612
	107.3165	34.0621		w_124			AB	2.9			99.18		13.6		2 781 072
	107.3165	34.0621		w_125			AB	2.9			90.12		12.0		3 076 129
陕西省汉中市略阳县	106.1635	33.3351		w_126			AB	3.2			99.48		11.7		2 911 427
Lueyang County，Hanzhong，	106.1635	33.3351		w_127			AB	3.1			98.20		13.7		2 829 702
Shaanxi	106.1635	33.3351		w_128			AB	3.0			98.93		12.9		3 242 280
陕西省宝鸡市太白县 Taibai County，Baoji， Shaanxi	107.3165	34.0621		w_129			A	1.9
	107.3165	34.0621		w_130			A	1.8
	107.3056	34.1321		w_131			A	2.5
	107.3056	34.1321		w_132			A	2.3
陕西省汉中市洋县 Yang County，Hanzhong， Shaanxi	107.3056	34.1321		w_133			A	—
陕西省安康市镇坪县 Zhenping County，Ankang， Shaanxi	109.5479	31.8479		w_134			A	—
云南省庆迪州维西县 Weixi County，Qingdi， Yunnan	99.1961	27.1831		w_135			A	2.2
	99.1961	27.1831		w_136			A	2.4
	99.1961	27.1831		w_137			A	—
	99.1961	27.1831		w_138			A	2.2
	99.1961	27.1831		w_139			A	2.1
	99.1961	27.1831		w_140			A	2.2
	99.1961	27.1831		w_141			A	—
浙江省杭州市临安区 Lin’'an County， Hangzhou，Zhejiang	119.4547	30.3225		w_142			AB	2.6			99.12		12.5		3 206 724
	119.4547	30.3225		w_143			AB	2.5			99.35		12.0		3 013 453
	119.4492	30.3117		w_144			AB	2.3			98.82		13.2		3 109 326
	119.4492	30.3117		w_145			AB	2.1			97.89		11.2		2 890 372
	119.4492	30.3117		w_146			AB	1.8			99.27		12.8		3 171 401
重庆市巫山县	109.8802	31.3034		w_147				—
Wushan County，Chongqing	109.8802	31.3034		w_148				—
贵州省铜仁市玉屏县	108.9187	27.3343		w_149				—
Yuping County， Tongren，Guizhou	108.9187	27.3343		w_150				—
Yuping County， Tongren，Guizhou	108.8399	27.3384		w_151				—
河南省信阳市新县 Xin County，Xinyang，Henan	114.7692	31.7145		w_152				—
河南省信阳市新县 Xin County，Xinyang，Henan	114.7692	31.7145		w_153				—
北京怀柔 Huairou，Beijing				c_001		怀黄Huaihuang	AB				98.68		13.4		3 992 779
北京怀柔 Huairou，Beijing				c_002		燕丰Yanfeng	A
河北遵化 Zunhua，Hebei				c_003		北峪2号Beiyu 2	AB				98.59		12.2		4 048 619
北京昌平 Changping，Beijing				c_004		燕红Yanhong	AB				96.45		12.0		3 940 059
河北遵化 Zunhua，Hebei			c_005		燕晶Yanjing		A
北京密云 Miyun，Beijing			c_006		短花云丰 Duanhua Yunfeng		AB				97.92		11.4			3 947 272
北京昌平 Changping，Beijing			c_007		黑山寨7号 Heishanzhai 7		AB				97.95		13.0			4 048 159
河北青龙 Qinglong，Hebei			c_008		燕秋Yanqiu		A
河北迁西 Qianxi,Hebei			c_009		燕山短枝 Yanshan Duanzhi		AB				99.05		13.6			4 051 254
北京怀柔 Huairou，Beijing			c_010		怀九Huaijiu		A
河北青龙 Qinglong，Hebei			c_011		燕紫Yanzi		A
山东莒南 Junan，Shangdong			c_012		沂蒙短枝 Yimeng Duanzhi		A
山东莒南 Junan，Shangdong			c_013		沂南薄壳 YinanBoke		A
江苏宜兴 Yixing，Anhui			c_014		处暑红 Chushuhong		A
山东莱阳 Laiyang，Shangdong			c_015		玉丰Yufeng		A
山东乳山 Rushan，Shangdong			c_016		枣林Zaolin		A
山东乳山 Rushan，Shangdong			c_017		枣林13号 Zaolin 13		A
陕西镇安 Zhenan，Shaanxi			c_018		柞14 Zha 14		A
陕西镇安 Zhenan，Shaanxi			c_019		柞18 Zha 18		A
山东泰安 Shangdong			c_020		黄棚Huangpeng		AB				97.48		12.1			3 937 769
陕西镇安 Zhenan，Shaanxi			c_021		柞红栗Zhahongli		A
陕西镇安 Zhenan，Shaanxi			c_022		柞水11号 Zhashui 11		A
山东泰安 Tai’an，Shangdong			c_023		黄前无花 Huangqian Wuhua		A
山东临沂 Linyi，Shandong			c_024		垂枝2号 Chuizhi 2		A
湖北罗田 Luotian，Hubei			c_025		薄壳大油栗 Boke Dayouli		AB				96.58		11.8			4 056 334
河北宽城 Kuancheng，Hebei			c_026		大板红Dabanhong		A
山东泰安 Tai’an，Shangdong			c_027		岱岳早丰 Daiyue Zaofeng		A
北京怀柔 Huairou，Beijing			c_028		京暑红 Jingshuhong		AB				98.65		13.6			4 032 301
山东泰安 Tai’an，Shangdong			c_029		东岳早丰 Dongyue Zaofeng		A
山东海阳 Haiyang，Shangdong			c_030		海丰Haifeng		A
山东莱西 Laixi，Shangdong			c_031		红光栗 Hongguangli		AB				99.05		12.2			4 034 636
山东泰安 Tai’an，Shangdong			c_032		山东红栗 Shandonghongli		AB				98.00		11.8			4 038 779
山东招远 Zhaoyuan， Shangdong			c_033		金丰Jinfeng		A
山东泰安 Tai’an，Shangdong			c_034		华丰Huafeng		A
山东泰安 Tai’an，Shangdong			c_035		华光Huaguang		A
山东烟台 Yantai，Shangdong			c_036		上丰Shangfeng		A
山东海阳 Haiyang，Shangdong			c_037		石丰Shifeng		A
山东烟台 Yantai，Shangdong			c_038		烟清Yanqing		A
山东烟台 Yantai，Shangdong			c_039		烟泉Yanquan		A
河北青龙 Qinglong，Hebei			c_040		燕宝Yanbao		A
湖北罗田 Luotian，Hubei			c_041		羊毛栗Yangmaoli		A
山东泰安 Tai’an，Shangdong			c_042		中明栗 Zhongmingli		A
湖北麻城Macheng，Hubei			c_043		鄂栗1号Eli 1		A
湖北罗田 Luotian，Hubei			c_044		桂花栗Guihuali		A
湖北罗田 Luotian，Hubei			c_045		桂花香 Guihuaxiang		A
湖北罗田 Luotian，Hubei			c_046		六月爆Liuyuebao		AB				98.60		12.8			3 800 795
广东韶关 Shaoguan，Guangdong			c_047		韶栗18号 Shaoli 18		A
湖北罗田 Luotian，Hubei			c_048		浅刺大板栗 QianciDabanli		AB				99.24		11.5			4 055 864

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