Genetic Evolution and Taxonomic Status Analysis of Wild Citrus Resources Based on Resequencing in Guposhan Mountain in Guangxi Province

doi:10.16420/j.issn.0513-353x.2021-0058

Acta Horticulturae Sinica ›› 2022, Vol. 49 ›› Issue (2): 407-415.doi: 10.16420/j.issn.0513-353x.2021-0058

• Research Notes • Previous Articles Next Articles

Genetic Evolution and Taxonomic Status Analysis of Wild Citrus Resources Based on Resequencing in Guposhan Mountain in Guangxi Province

WU Xiaoxiao, CHEN Chuanwu, LIU Ping, TANG Yan, DENG Chongling()

Guangxi Citrus Breeding and Cultivation Research Center of Engineering Technology,Guangxi Academy of Specialty Crops,Guilin,Guangxi 541004,China

Received:2021-05-20 Revised:2021-12-17 Online:2022-02-25 Published:2022-02-28
Contact: DENG Chongling E-mail:cldeng88168@126.com

Abstract

Abstract:

Analyzing the genetic evolution and taxonomic status of wild citrus resources in Guposhan Mountain in Guangxi Province,provides a theoretical basis for citrus germplasm innovation and genetic improvement,and also provides a basis for in-depth exploration of genes related to excellent traits in the future. Whole genome sequencing was performed on four wild citrus varieties from Guposhan Mountain in Guangxi,one Poncirus trifoliata,one kumquat,and 14 other citrus. The amount of sequencing data for each sample was about 16 Gb,and the average sequencing depth was 54×. Through short read mapping,SNP detection,PCA principal component analysis,and neighbor joining method to construct a phylogenetic tree,reveal its genetic diversity and population genetic structure. From 20 samples,6 782 158 high-quality SNP loci were detected. Based on these SNP sites,and according to the PCA principal component analysis and phylogenetic tree analysis results,20 samples can be divided into three categories： wild citrus in Guposhan and C. mangshanensis are clustered together,and kumquat and other citrus are clustered together. Poncirus trifoliata is a separate category. The study analyzed the genetic diversity and population evolution of wild citrus resources in Guposhan Mountain from the whole genome level,and showed that wild citrus resources in Guposhan Mountain are primitive and unique like C. mangshanensis. They are supposed to be an independent and true species within the genus citrus,or it is a separate genus other than Poncirus,Fortunella Swing and Citrus L.

Key words: citrus, genome, evolution, diversity

CLC Number:

S666

WU Xiaoxiao, CHEN Chuanwu, LIU Ping, TANG Yan, DENG Chongling. Genetic Evolution and Taxonomic Status Analysis of Wild Citrus Resources Based on Resequencing in Guposhan Mountain in Guangxi Province[J]. Acta Horticulturae Sinica, 2022, 49(2): 407-415.

Figures/Tables 7

References 35

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名称 Name	叶身 leaf shape	叶尖 Leaf tip	叶基 Leaf base	叶缘 Leaf margin	叶柄长/cm Petiole length	叶片长/cm Leaf length	叶片宽/cm Leaf width	叶形指数 Leaf type index
皱皮柑2号 Zhoupigan 2	圆形 Round	钝圆 Blunt round	广楔形 Wide wedge	锯齿缘 Serrated edge	0.87 ± 0.21	4.24 ± 0.85	2.32 ± 0.32	1.83 ± 0.27
皱皮柑5号 Zhoupigan 5	菱形 Diamond	钝圆 Blunt round	楔形 Wedge	全缘 All edge	0.96 ± 0.16	4.25 ± 0.92	2.29 ± 0.24	1.86 ± 0.43
皱皮柑6号 Zhoupigan 6	菱形 Diamond	钝圆 Blunt round	楔形 Wedge	全缘 All edge	1.00 ± 0.25	5.41 ± 0.93	2.77 ± 0.58	1.95 ± 0.20
姑婆山野生元橘 Sinocitrus chuana	菱形 Diamond	短尖 short-pointed	狭楔形 Narrow wedge	浅波缘 Shallow edge	0.92 ± 0.13	4.85 ± 0.56	2.32 ± 0.19	2.09 ± 0.33

名称 Name	叶身 leaf shape	叶尖 Leaf tip	叶基 Leaf base	叶缘 Leaf margin	叶柄长/cm Petiole length	叶片长/cm Leaf length	叶片宽/cm Leaf width	叶形指数 Leaf type index
皱皮柑2号 Zhoupigan 2	圆形 Round	钝圆 Blunt round	广楔形 Wide wedge	锯齿缘 Serrated edge	0.87 ± 0.21	4.24 ± 0.85	2.32 ± 0.32	1.83 ± 0.27
皱皮柑5号 Zhoupigan 5	菱形 Diamond	钝圆 Blunt round	楔形 Wedge	全缘 All edge	0.96 ± 0.16	4.25 ± 0.92	2.29 ± 0.24	1.86 ± 0.43
皱皮柑6号 Zhoupigan 6	菱形 Diamond	钝圆 Blunt round	楔形 Wedge	全缘 All edge	1.00 ± 0.25	5.41 ± 0.93	2.77 ± 0.58	1.95 ± 0.20
姑婆山野生元橘 Sinocitrus chuana	菱形 Diamond	短尖 short-pointed	狭楔形 Narrow wedge	浅波缘 Shallow edge	0.92 ± 0.13	4.85 ± 0.56	2.32 ± 0.19	2.09 ± 0.33

名称 Name	着生 Implantation position	花粉量 Pollen quantity	花丝 Filament state	花瓣数 Number of petals	花瓣长/cm Petals length	花瓣宽/cm Petal width	雄蕊数/个 Number of stamens	花丝长/cm Filaments length	花柱长/cm Style length
皱皮柑2号 Zhoupigan 2	丛生 Cluster state	中等 Moderate	分离 Separate	4.95 ± 0.22	1.28 ± 0.10	0.68 ± 0.05	22.88 ± 1.32	0.75 ± 0.07	0.14 ± 0.09
皱皮柑5号 Zhoupigan 5	丛生 Cluster state	多 Abundant	分离 Separate	4.95 ± 0.37	1.18 ± 0.08	0.67 ± 0.08	22.10 ± 1.65	0.66 ± 0.07	0.11 ± 0.04
皱皮柑6号 Zhoupigan 6	丛生 Cluster state	中等 Moderate	分离 Separate	4.67 ± 0.47	1.72 ± 0.14	0.68 ± 0.07	24.10 ± 2.12	1.09 ± 0.09	0.83 ± 0.31
姑婆山野生元橘 Sinocitrus chuana	单生 Solitary state	中等 Moderate	部分联合 Partial union	4.53 ± 0.40	0.94 ± 0.14	0.48 ± 0.04	23.12 ± 0.63	0.56 ± 0.18	0.14 ± 0.09

名称 Name	着生 Implantation position	花粉量 Pollen quantity	花丝 Filament state	花瓣数 Number of petals	花瓣长/cm Petals length	花瓣宽/cm Petal width	雄蕊数/个 Number of stamens	花丝长/cm Filaments length	花柱长/cm Style length
皱皮柑2号 Zhoupigan 2	丛生 Cluster state	中等 Moderate	分离 Separate	4.95 ± 0.22	1.28 ± 0.10	0.68 ± 0.05	22.88 ± 1.32	0.75 ± 0.07	0.14 ± 0.09
皱皮柑5号 Zhoupigan 5	丛生 Cluster state	多 Abundant	分离 Separate	4.95 ± 0.37	1.18 ± 0.08	0.67 ± 0.08	22.10 ± 1.65	0.66 ± 0.07	0.11 ± 0.04
皱皮柑6号 Zhoupigan 6	丛生 Cluster state	中等 Moderate	分离 Separate	4.67 ± 0.47	1.72 ± 0.14	0.68 ± 0.07	24.10 ± 2.12	1.09 ± 0.09	0.83 ± 0.31
姑婆山野生元橘 Sinocitrus chuana	单生 Solitary state	中等 Moderate	部分联合 Partial union	4.53 ± 0.40	0.94 ± 0.14	0.48 ± 0.04	23.12 ± 0.63	0.56 ± 0.18	0.14 ± 0.09

样品编号 Sample	资源 Resource	总Reads数 Total reads	总碱基数/bp Total base	比对Reads数 Comparison reads	总比对率/% Total ratio	双端比对率/% Double-terminal ratio	平均测序深度（×） Average sequencing depth
S01	枳Poncirus trifoliata	107 697 496	16 154 624 400	99 286 290	92.19	76.67	53.60
S02	阳朔金柑Fortunella ‘Yangshuo Jingan’	89 529 554	13 429 433 100	83 875 162	93.68	79.89	44.56
S03	红河大翼橙 Citrus hongheensis	98 195 835	14 729 375 250	90 439 245	92.10	78.80	48.88
S04	龙胜小江村宜昌橙 C. ichangensis ‘Longsheng Xiaojiangcun’	109 088 887	16 363 333 050	103 907 427	95.25	81.29	54.30
S05	莽山野柑（尖叶） C. mangshanensis （pointed leaf）	107 753 893	16 163 083 950	103 036 387	95.62	81.53	53.63
S06	莽山野柑（圆叶） C. mangshanensis （round leaf）	103 687 777	15 553 166 550	99 627 681	96.08	82.54	51.61
S07	姑婆山野生皱皮柑2号 Guposhan Wild Zhoupigan 2	103 255 191	15 488 278 650	98 252 313	95.15	81.28	51.39
S08	姑婆山野生皱皮柑5号 Guposhan Wild Zhoupigan 5	118 238 006	17 735 700 900	110 819 337	93.73	79.74	58.85
S09	姑婆山野生皱皮柑6号 Guposhan Wild Zhoupigan 6	92 758 407	13 913 761 050	85 643 147	92.33	78.24	46.17
S10	姑婆山野生元橘 Sinocitrus chuana Tseng	112 921 407	16 938 211 050	107 256 623	94.98	81.75	56.21
S11	道县野橘C. daoxianensis	107 933 335	16 190 000 250	104 004 963	96.36	88.68	53.72
S12	立花橘C. tachibana	109 720 035	16 458 005 250	105 353 025	96.02	86.90	54.61
S13	印度野橘C. reshni	109 206 848	16 381 027 200	103 799 050	95.05	77.84	54.36
S14	岑溪酸橘 C. reticulata Cenxi Suanju	109 748 912	16 462 336 800	104 143 887	94.89	89.17	54.63
S15	猫儿山野橘C. reticulata Maoershan Yeju	99 806 304	14 970 945 600	95 741 594	95.93	88.23	49.68
S16	沙柑C. nobilis Lour	109 428 871	16 414 330 650	105 720 169	96.61	88.43	54.47
S17	新会橙C. sinensis ‘Xinhuicheng’	126 858 264	19 028 739 600	116 928 159	92.17	83.69	63.14
S18	沙田柚 C. grandis Shatianyou	106 098 668	15 914 800 200	99 741 325	94.01	80.25	52.81
S19	里斯本柠檬 C. limon Lisbon Lemon	112 169 164	16 825 374 600	106 248 936	94.72	80.82	55.83
S20	广佛手 C. medica Guangfoshou	116 115 073	17 417 260 950	110 689 088	95.33	78.15	57.79

Genetic Evolution and Taxonomic Status Analysis of Wild Citrus Resources Based on Resequencing in Guposhan Mountain in Guangxi Province

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样品编号 Sample	资源 Resource	位点数 Number of site	纯合数（%） Homo	杂合数（%） Hete
S01	枳Poncirus trifoliata	5 342 092	4 003 999（74.95）	1 338 093（25.05）
S02	阳朔金柑Fortunella‘Yangshuo Jingan’	4 661 269	2 846 563（61.07）	1 814 706（38.93）
S03	红河大翼橙Citrus hongheensis	4 165 337	2 906 844（69.79）	1 258 493（30.21）
S04	龙胜小江村宜昌橙C. ichangensis‘Longsheng Xiaojiangcun’	3 879 284	2 908 068（74.96）	971 216（25.04）
S05	莽山野柑（尖叶）C. mangshanensis（pointed leaf）	4 820 706	3 348 887（69.47）	1 471 819（30.53）
S06	莽山野柑（圆叶）C. mangshanensis（round leaf）	4 841 588	3 344 729（69.08）	1 496 859（30.92）
S07	姑婆山野生皱皮柑2号Guposhan Wild Zhoupigan 2	4 738 800	3 426 441（72.31）	1 312 359（27.69）
S08	姑婆山野生皱皮柑5号Guposhan Wild Zhoupigan 5	4 840 706	3 380 071（69.83）	1 460 635（30.17）
S09	姑婆山野生皱皮柑6号Guposhan Wild zhoupigan 6	4 730 027	3 400 590（71.89）	1 329 437（28.11）
S10	姑婆山野生元橘Sinocitrus chuana Tseng	4 746 218	3 406 565（71.77）	1 339 653（28.23）
S11	道县野橘C. daoxianensis	2 254 695	988 458（43.84）	1 266 237（56.16）
S12	立花橘C. tachibana	2 606 981	835 629（32.05）	1 771 352（67.95）
S13	印度野橘C. reshni	4 695 910	3 771 979（80.32）	923 931（19.68）
S14	岑溪酸橘C. reticulata Cenxi Suanju	1 801 567	733 504（40.71）	1 068 063（59.29）
S15	猫儿山野橘C. reticulata Maoershan Yeju	2 248 710	645 918（28.72）	1 602 792（71.28）
S16	沙柑C. nobilis Lour	2 688 157	379 017（14.10）	2 309 140（85.90）
S17	新会橙C. sinensis Xinhuicheng	3 612 044	348 953（9.66）	3 263 091（90.34）
S18	沙田柚C. grandis Shatianyou	4 225 856	2 743 552（64.92）	1 482 304（35.08）
S19	里斯本柠檬C. limon Lisbon Lemon	5 537 457	1 323 345（23.90）	4 214 112（76.10）
S20	广佛手C. medica Guangfoshou	5 149 649	3 863 235（75.02）	1 286 414（24.98）

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