Genetic diversity analysis of Trapa L. cultivars in Jiangsu and Zhejiang Provinces using SLAF-seq

doi:10.3969/j.issn.1004-1524.20220965

Acta Agriculturae Zhejiangensis ›› 2023, Vol. 35 ›› Issue (8): 1773-1781.DOI: 10.3969/j.issn.1004-1524.20220965

• Horticultural Science • Previous Articles Next Articles

Genetic diversity analysis of Trapa L. cultivars in Jiangsu and Zhejiang Provinces using SLAF-seq

YUAN Ye¹(), LIU Rui², WANG Lingyun³, SHEN Meng¹, YE Xuelian², QUAN Xinhua¹, WANG Ruisen¹, YAO Xiangtan¹^,^*()

1. Jiaxing Academy of Agricultural Sciences, Jiaxing 314016, Zhejiang, China
2. Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China
3. Provincial Key Laboratory of Characteristic Aquatic Vegetable Breeding and Cultivation, Jinhua Academy of Agricultural Sciences/Zhejiang Institute of Agricultural Machinery, Jinhua 321000, Zhejiang, China

Received:2022-06-28 Online:2023-08-25 Published:2023-08-29

Abstract

Abstract:

By using SLAF-seq technology, 17 main cultivated varieties and one wild variety of Trapa L. in Jiangsu and Zhejiang areas were high-throughput sequenced, 445 594 SLAF tags were obtained, and 95 931 polymorphic SLAF tags were identified. A total of 269 338 SNP markers obtained were used to construct the phylogenetic tree and analyze the population structure for the 18 samples of Trapa L. The results showed that SLAF-seq technology could efficiently develop a large number of SNP markers which could be used for population genetic analysis. Different types of Trapa L. were distinguished well by the SNP-based phylogenetic analysis. These results provided a reference for the further identification of germplasm resources and the research on the genetic evolution of Trapa L.

Key words: Trapa L., genetic diversity, specific-locus amplified fragment sequencing, single nucleotide polymorphism

CLC Number:

S645.4

YUAN Ye, LIU Rui, WANG Lingyun, SHEN Meng, YE Xuelian, QUAN Xinhua, WANG Ruisen, YAO Xiangtan. Genetic diversity analysis of Trapa L. cultivars in Jiangsu and Zhejiang Provinces using SLAF-seq[J]. Acta Agriculturae Zhejiangensis, 2023, 35(8): 1773-1781.

Figures/Tables 7

References 28

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样品Sample	品种名Name of variety	类别Variety type	原产地Source area
aa	南湖菱Nanhuling	无角菱Trapa acornis Nakai	嘉兴Jiaxing
ab	无角青菱Wujiaoqingling	无角菱Trapa acornis Nakai	嘉兴Jiaxing
ac	环菱1 Huanling 1	乌菱Trapa bicornis Nakai	嘉兴Jiaxing
ad	环菱2 Huanling 2	乌菱Trapa bicornis Nakai	宿迁Suqian
ae	环菱3 Huanling 3	乌菱Trapa bicornis Nakai	宿迁Suqian
af	苏州青菱Suzhouqingling	四角菱Trapa quadrispinosa Roxb.	苏州Suzhou
ag	邵伯菱Shaoboling	四角菱Trapa quadrispinosa Roxb.	扬州Yangzhou
ah	野菱Yeling	野菱Trapa incisa Sieb	嘉兴Jiaxing
ai	金华青菱Jinhuaqingling	四角菱Trapa quadrispinosa Roxb.	金华Jinhua
aj	绍兴水红菱1 Shaoxingshuihongling 1	四角菱Trapa quadrispinosa Roxb.	嘉兴Jiaxing
ak	两角红菱Liangjiaohongling	二角菱Trapa bispinosa Roxb.	嘉兴Jiaxing
al	水果红菱Shuiguohongling	二角菱Trapa bispinosa Roxb.	苏州Suzhou
am	南湖红菱Nanhuhongling	无角菱Trapa acornis Nakai	嘉兴Jiaxing
an	驼背白菱Tuobeibailing	四角菱Trapa quadrispinosa Roxb.	绍兴Shaoxing
ao	嘉兴水红菱Jiaxingshuihongling	四角菱Trapa quadrispinosa Roxb.	嘉兴Jiaxing
ap	南湖菱提纯Nanhulingtichun	无角菱Trapa acornis Nakai	嘉兴Jiaxing
aq	绍兴水红菱2 Shaoxingshuihongling 2	四角菱Trapa quadrispinosa Roxb.	绍兴Shaoxing
ar	两角青菱Liangjiaoqingling	二角菱Trapa bispinosa Roxb.	嘉兴Jiaxing

样品Sample	品种名Name of variety	类别Variety type	原产地Source area
aa	南湖菱Nanhuling	无角菱Trapa acornis Nakai	嘉兴Jiaxing
ab	无角青菱Wujiaoqingling	无角菱Trapa acornis Nakai	嘉兴Jiaxing
ac	环菱1 Huanling 1	乌菱Trapa bicornis Nakai	嘉兴Jiaxing
ad	环菱2 Huanling 2	乌菱Trapa bicornis Nakai	宿迁Suqian
ae	环菱3 Huanling 3	乌菱Trapa bicornis Nakai	宿迁Suqian
af	苏州青菱Suzhouqingling	四角菱Trapa quadrispinosa Roxb.	苏州Suzhou
ag	邵伯菱Shaoboling	四角菱Trapa quadrispinosa Roxb.	扬州Yangzhou
ah	野菱Yeling	野菱Trapa incisa Sieb	嘉兴Jiaxing
ai	金华青菱Jinhuaqingling	四角菱Trapa quadrispinosa Roxb.	金华Jinhua
aj	绍兴水红菱1 Shaoxingshuihongling 1	四角菱Trapa quadrispinosa Roxb.	嘉兴Jiaxing
ak	两角红菱Liangjiaohongling	二角菱Trapa bispinosa Roxb.	嘉兴Jiaxing
al	水果红菱Shuiguohongling	二角菱Trapa bispinosa Roxb.	苏州Suzhou
am	南湖红菱Nanhuhongling	无角菱Trapa acornis Nakai	嘉兴Jiaxing
an	驼背白菱Tuobeibailing	四角菱Trapa quadrispinosa Roxb.	绍兴Shaoxing
ao	嘉兴水红菱Jiaxingshuihongling	四角菱Trapa quadrispinosa Roxb.	嘉兴Jiaxing
ap	南湖菱提纯Nanhulingtichun	无角菱Trapa acornis Nakai	嘉兴Jiaxing
aq	绍兴水红菱2 Shaoxingshuihongling 2	四角菱Trapa quadrispinosa Roxb.	绍兴Shaoxing
ar	两角青菱Liangjiaoqingling	二角菱Trapa bispinosa Roxb.	嘉兴Jiaxing

样品 Sample	总序列数 Total reads	GC含量 GC content/%	测序质量Q30 Q30 percentage/%
aa	2 932 097	41.32	89.9
ab	2 596 064	41.40	89.77
ac	3 570 364	41.17	89.81
ad	2 198 670	41.14	89.74
ae	4 671 291	41.19	91.58
af	4 263 822	41.49	90.55
ag	2 283 401	41.07	91.97
ah	3 040 597	40.72	92.19
ai	2 942 299	40.72	92.82
aj	3 024 718	40.62	92.36
ak	3 519 849	42.23	92.95
al	3 488 184	41.95	90.74
am	3 070 469	41.61	92.69
an	2 546 657	40.93	92.34
ao	1 640 283	41.40	92.64
ap	3 001 143	41.22	92.7
aq	2 141 727	41.13	92.52
ar	3 413 097	42.42	93.00
Rice	1 218 766	43.87	90.09

样品 Sample	总序列数 Total reads	GC含量 GC content/%	测序质量Q30 Q30 percentage/%
aa	2 932 097	41.32	89.9
ab	2 596 064	41.40	89.77
ac	3 570 364	41.17	89.81
ad	2 198 670	41.14	89.74
ae	4 671 291	41.19	91.58
af	4 263 822	41.49	90.55
ag	2 283 401	41.07	91.97
ah	3 040 597	40.72	92.19
ai	2 942 299	40.72	92.82
aj	3 024 718	40.62	92.36
ak	3 519 849	42.23	92.95
al	3 488 184	41.95	90.74
am	3 070 469	41.61	92.69
an	2 546 657	40.93	92.34
ao	1 640 283	41.40	92.64
ap	3 001 143	41.22	92.7
aq	2 141 727	41.13	92.52
ar	3 413 097	42.42	93.00
Rice	1 218 766	43.87	90.09

样品 Sample	SLAF标签数 SLAF number	测序总深度 Total depth	平均深度 Average depth
aa	166 455	2 767 290	16.62
ab	177 000	2 424 843	13.70
ac	186 372	3 375 654	18.11
ad	145 281	1 989 982	13.70
ae	219 199	4 463 382	20.36
af	199 132	4 033 069	20.25
ag	186 738	2 144 672	11.48
ah	220 713	2 817 050	12.76
ai	202 101	2 821 259	13.96
aj	200 880	2 901 428	14.44
ak	239 781	3 370 804	14.06
al	208 188	3 261 502	15.67
am	243 534	2 848 883	11.70
an	198 748	2 421 674	12.18
ao	164 538	1 556 854	9.46
ap	217 485	2 874 677	13.22
aq	210 247	2 024 107	9.63
ar	253 900	3 187 561	12.55

Genetic diversity analysis of Trapa L. cultivars in Jiangsu and Zhejiang Provinces using SLAF-seq

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样品 Sample	SNP总数 Total SNP	对应SNP个数 SNP number	SNP杂合率 Hetloci ratio/%	SNP完整度 Integrity ratio/%
aa	269 338	169 049	1.75	62.76
ab	269 338	180 913	2.13	67.16
ac	269 338	181 016	1.97	67.20
ad	269 338	167 124	2.96	62.04
ae	269 338	212 843	4.03	79.02
af	269 338	199 091	2.46	73.91
ag	269 338	191 099	2.25	70.95
ah	269 338	209 631	51.32	77.83
ai	269 338	205 872	2.72	76.43
aj	269 338	199 054	2.14	73.90
ak	269 338	212 032	2.70	78.72
al	269 338	206 130	6.19	76.53
am	269 338	224 360	6.70	83.30
an	269 338	196 836	1.88	73.08
ao	269 338	177 757	1.59	65.99
ap	269 338	206 121	2.28	76.52
aq	269 338	201 976	2.47	74.98
ar	269 338	223 897	3.81	83.12

样品Sample	Q1	Q2	Q3	Q4	Q5	Q6	Q7	组Group
af	0.999 934	0.000 010	0.000 016	0.000 010	0.000 010	0.000 010	0.000 010	Q1
ak	0.488 402	0.000 010	0.188 437	0.076 140	0.223 630	0.023 371	0.000 010	Q1
aa	0.000 010	0.999 940	0.000 010	0.000 010	0.000 010	0.000 010	0.000 010	Q2
ag	0.000 014	0.616 692	0.000 010	0.383 254	0.000 010	0.000 010	0.000 010	Q2
ap	0.000 010	0.999 940	0.000 010	0.000 010	0.000 010	0.000 010	0.000 010	Q2
al	0.000 010	0.000 010	0.999 940	0.000 010	0.000 010	0.000 010	0.000 010	Q3
ar	0.000 010	0.000 010	0.999 940	0.000 010	0.000 010	0.000 010	0.000 010	Q3
ai	0.000 010	0.000 010	0.020 474	0.375 273	0.249 194	0.355 028	0.000 010	Q4
aj	0.000 010	0.000 010	0.000 010	0.999 940	0.000 010	0.000 010	0.000 010	Q4
an	0.000 010	0.000 010	0.000 010	0.999 940	0.000 010	0.000 010	0.000 010	Q4
af	0.000 010	0.000 010	0.000 010	0.999 940	0.000 010	0.000 010	0.000 010	Q4
aq	0.000 010	0.000 010	0.000 010	0.999 940	0.000 010	0.000 010	0.000 010	Q4
ac	0.000 010	0.000 010	0.000 010	0.000 010	0.999 940	0.000 010	0.000 010	Q5
ad	0.000 010	0.000 010	0.000 010	0.000 010	0.999 940	0.000 010	0.000 010	Q5
ae	0.000 010	0.000 010	0.000 010	0.000 010	0.999 940	0.000 010	0.000 010	Q5
ab	0.000 015	0.000 010	0.000 010	0.000 010	0.000 010	0.999 935	0.000 010	Q6
am	0.000 010	0.000 220	0.000 010	0.000 010	0.000 010	0.999 730	0.000 010	Q6
ah	0.000 010	0.000 010	0.000 010	0.000 010	0.000 010	0.000 010	0.999 940	Q7

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[11]	WANG Baogen, DONG Junyang, WANG Ying, LI Sujuan, WANG Jian, LU Zhongfu, WU Xiaohua, LI Guojing, WU Xinyi. Evaluation and genetic diversity analysis of common bean germplasm in Zhejiang Province, China [J]. Acta Agriculturae Zhejiangensis, 2022, 34(11): 2416-2427.
[12]	LU Yanhui, GUO Jiawen, TIAN Junce, XUE Zhaohong, ZHENG Xusong, LYU Zhongxian. Population genetic structure of different resistance levels of Chilo suppressalis based on mitochondrial COⅠ and Cytb sequences in Zhejiang, China [J]. Acta Agriculturae Zhejiangensis, 2022, 34(11): 2462-2470.
[13]	WANG Zhiqi, SUN Jian, LIANG Junchao, ZHAO Yunyan, YAN Tingxian, YAN Xiaowen, WEI Wenliang, LE Meiwang. Study on genetic diversity of sesame germplasm in Jiangxi Province based on molecular markers [J]. Acta Agriculturae Zhejiangensis, 2021, 33(9): 1565-1580.
[14]	MA Jie, QU Wen, CHEN Chunyan, WANG Lei, MA Jun, LIU Zhenshan, MA Wei, ZHOU Ping, HE Yuankuan, SUN Bo. Development of SSR markers based on transcriptome sequencing and genetic diversity analysis of Nainaiqingcai leaf mustard [J]. Acta Agriculturae Zhejiangensis, 2021, 33(9): 1640-1649.
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