Whole Genome Resequencing Analysis of‘Cuihongli’Plum and Its Early-Ripening Bud Sport Mutation

doi:10.16420/j.issn.0513-353x.2023-0799

Acta Horticulturae Sinica ›› 2024, Vol. 51 ›› Issue (10): 2255-2266.doi: 10.16420/j.issn.0513-353x.2023-0799

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

Whole Genome Resequencing Analysis of‘Cuihongli’Plum and Its Early-Ripening Bud Sport Mutation

YAO Yuan¹, DENG Lijun¹, HU Juan², TANG Xiaoyu¹, WANG Tie¹, LI Hang¹, SUN Guochao¹, XIONG Bo¹, LIAO Ling¹, WANG Zhihui¹^,^*()

¹ College of Horticulture，Sichuan Agricultural University，Chengdu 611130，China
² Pujiang County Agriculture and Rural Bureau，Pujiang，Sichuan 611600，China

Received:2024-05-30 Revised:2024-08-08 Online:2024-12-13 Published:2024-10-21
Contact: WANG Zhihui

Abstract

Abstract:

In order to reveal the molecular basis of formation of‘Cuihongli’plum’s early-ripening bud sport mutation，this study used high-throughput re-sequencing technology to resequence the whole genomes of‘Cuihongli’and its early-ripening bud sport mutation，with an average sequencing depth of 19.40× and 22.82×，with a genome coverage of over 85%. The results showed compared with the reference genome，1 860 745 and 1 931 603 single nucleotide polymorphisms（SNPs），419 134 and 444 892 small fragment insertion/deletion sites（InDels）were detected in‘Cuihongli’and its early-ripening bud sport mutation. There are 61 997 and 63 498 nonsynonymous mutations in the coding region，causing a total of 2 391 gene mutations. Metabolic pathway analysis（KEGG）indicated that these genetic variations were mainly involved in the pathways of Ribosome biogenesis in eukaryotes，RNA transport，phenylpropanoid biosynthesis and plant-pathogen interaction. In addition，12 variant genes were annotated with functions in the plant hormone signal transduction pathway. These genes and other related genes variations can affect the activity or specificity of their corresponding proteins or enzymes，leading to changes in the growth and development process，and advancing the mature period of‘Cuihongli’plum’s early-ripening single plant.

Key words: plum, bud sport mutation, early-ripening, whole genome re-sequencing

YAO Yuan, DENG Lijun, HU Juan, TANG Xiaoyu, WANG Tie, LI Hang, SUN Guochao, XIONG Bo, LIAO Ling, WANG Zhihui. Whole Genome Resequencing Analysis of‘Cuihongli’Plum and Its Early-Ripening Bud Sport Mutation[J]. Acta Horticulturae Sinica, 2024, 51(10): 2255-2266.

Figures/Tables 11

References 32

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样品 Sample	原始测序序列 Raw read	过滤后剩余序列 Clean read	过滤剩余序列/% Clean reads rate	含N > 5%的Reads/% Ns reads rate	Q30/%	GC含量/% GC content
脆红李 Cuihongli	40 671 358	39 919 834	98.15	0.23	87.48	38.26
早熟芽变 Early-ripening mutant	47 401 654	46 638 688	98.39	0.22	88.45	38.31

样品 Sample	原始测序序列 Raw read	过滤后剩余序列 Clean read	过滤剩余序列/% Clean reads rate	含N > 5%的Reads/% Ns reads rate	Q30/%	GC含量/% GC content
脆红李 Cuihongli	40 671 358	39 919 834	98.15	0.23	87.48	38.26
早熟芽变 Early-ripening mutant	47 401 654	46 638 688	98.39	0.22	88.45	38.31

样品 Sample	Clean bases	Mapped bases	Mapped rate/%	Mean depth/×	Coverage 1×/%	Coverage 4×/%
脆红李 Cuihongli	5 987 975 100	5 513 839 633	92.08	19.40	92.03	85.67
早熟芽变 Early-ripening mutant	6 995 803 200	6 489 148 161	92.76	22.82	92.30	86.83

样品 Sample	Clean bases	Mapped bases	Mapped rate/%	Mean depth/×	Coverage 1×/%	Coverage 4×/%
脆红李 Cuihongli	5 987 975 100	5 513 839 633	92.08	19.40	92.03	85.67
早熟芽变 Early-ripening mutant	6 995 803 200	6 489 148 161	92.76	22.82	92.30	86.83

类别 Category	脆红李 Cuihongli	早熟芽变 Early-ripening mutant	差异数 Difference
总数 Total	1 860 745	1 931 603	70 858
基因间区 Intergenic	1 045 098（56.17%）	1 093 864（56.63%）	48 766
基因上游 Gene upstream	167 118（8.98%）	172 580（8.93%）	5 462
基因下游 Gene downstream	129 169（6.94%）	132 864（6.88%）	3 695
外显子 Exon	118 505（6.37%）	121 031（6.27%）	2 526
内含子 Intron	296 906（15.96%）	304 915（15.79%）	8 009
UTR5′	24 210（1.30%）	24 746（1.28%）	536
UTR3′	45 125（2.43%）	45 988（2.38%）	863
剪切区域 Splicing	434（0.02%）	464（0.02%）	30
其他 Others	34 180（1.83%）	35 151（1.82%）	971

Whole Genome Resequencing Analysis of‘Cuihongli’Plum and Its Early-Ripening Bud Sport Mutation

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Figures/Tables 11

References 32

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样品	转换	颠换	转换/颠换	纯合	杂合	杂合率/%
Sample	Transition	Transvertion	Ts/Tv	Homozygosity	Heterozygosity	Het-ratio
脆红李 Cuihongli	1 159 670	701 075	1.654	670 867	1 189 878	63.95
早熟芽变 Early-ripening mutant	1 204 261	727 342	1.656	683 247	1 248 356	64.63

样品	总数	非同义突变	同义突变	终止子出现	终止子缺失	未知类型
Sample	Total	Nonsynonymous	Synonymous	Stopgain	Stoploss	Unknown
脆红李 Cuihongli	118 505	61 997	55 029	1 005	256	218
早熟芽变 Early-ripening mutant	121 031	63 498	56 034	1 017	260	222
差异数 Difference	2 526	1 501	1 005	12	4	4

类别 Category	脆红李 Cuihongli	早熟芽变 Early-ripening mutant	差异数 Difference
总数 Total	419 134	444 892	25 758
基因间区 Intergenic	212 581（50.72%）	227 768（51.20%）	15 187
基因上游 Gene upstream	49 018（11.70%）	51 934（11.67%）	2 916
基因下游 Gene downstream	36 569（8.72%）	38 302（8.61%）	1 733
外显子 Exon	9 718（2.32%）	10 146（2.28%）	428
内含子 Intron	77 778（18.56%）	81 847（18.40%）	4 069
UTR5	9 246（2.21%）	9 628（2.16%）	382
UTR3	13 233（3.16%）	13 768（3.09%）	535
剪切区域 Splicing	273（0.07%）	292（0.07%）	19
其他 Others	10 718（2.54%）	11 207（2.52%）	489

样品 Sample	总数 Total	移码突变 Frameshift		非移码突变 Nonframeshift		终止子出现 Stopgain	终止子缺失 Stoploss	未知 Unknown
样品 Sample	总数 Total	插入 Insertion	缺失 Deletion	插入 Insertion	缺失 Deletion	终止子出现 Stopgain	终止子缺失 Stoploss	未知 Unknown
脆红李 Cuihongli	9 718	1 780	4 787	1 245	1 524	243	123	16
早熟芽变 Early-ripening mutant	10 146	1 867	4 954	1 338	1 576	262	129	20
差异数Difference	428	87	167	93	52	19	6	4

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