Gene Mapping of Plant Height in Papaya Based on BSA-seq

doi:10.13560/j.cnki.biotech.bull.1985.2025-0351

Abstract

Abstract:

Objective Plant height is one of the most important traits affecting the yield and quality of papaya (Carica papaya), and mapping the major candidate genes for papaya plant height provides genetic resources for the dwarf breeding of papaya. Method We used YY (taller plant) and GM (shorter plant) as the parents to construct a mapping population. The two parents and the offspring pools GY-H (taller pool) and GY-S (shorter pool) were then sequenced using BSA-seq technology. After the data were quality-controlled, the gene frequency gap between the pools was calculated by using the ED and SNP-index methods to locate the candidate intervals of the papaya plant height. Result The BSA-seq generated high-quality data, resulting in 337 980 SNP loci for gene mapping. The significant differences in genotype frequencies between the mixed pools were calculated using the ED and SNP-index methods, leading to the localization of candidate intervals with a size of 0.93 Mb on chromosome 3, 6, and 8. The interval was compared to the ‘Zihui’ papaya reference genome and found to contain 46 coding genes, 37 of which were annotated to various databases. Conclusion Cp_zihui12764, Cp_zihui06963, Cp_zihui07024, and Cp_zihui12732 are likely to be candidate genes to regulate the heights of the papaya plants.

Key words: Carica papaya, plant height, BSA-seq, gene mapping, candidate gene

WU Xia-ming, ZHOU Chen-ping, YANG Min, XU Ze, KUANG Rui-bin, LIU Chuan-he, HE Han, WEI Yue-rong. Gene Mapping of Plant Height in Papaya Based on BSA-seq[J]. Biotechnology Bulletin, 2025, 41(9): 54-61.

Figures/Tables 8

References 35

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样本名称Sample name	质控后 reads Clean reads	过滤后的碱基数Clean base （bp）	Q20 (%)	Q30 (%)	GC (%)	比对效率Mapped (%)	平均测序深度 Average depth (X)	10 × 覆盖率 Coverage ratio 10 × (%)
GM	57 631 310	8 615 217 987	97.98	94.94	36.52	99.38	24	90.48
YY	57 073 064	8 530 048 829	98.01	94.88	37.23	99.39	24	90.14
GY-S	90 185 416	13 468 978 624	97.98	94.81	37.05	98.20	38	95.87
GY-H	88 204 618	13 174 359 352	97.99	94.89	36.78	99.38	37	96.44

样本名称Sample name	质控后 reads Clean reads	过滤后的碱基数Clean base （bp）	Q20 (%)	Q30 (%)	GC (%)	比对效率Mapped (%)	平均测序深度 Average depth (X)	10 × 覆盖率 Coverage ratio 10 × (%)
GM	57 631 310	8 615 217 987	97.98	94.94	36.52	99.38	24	90.48
YY	57 073 064	8 530 048 829	98.01	94.88	37.23	99.39	24	90.14
GY-S	90 185 416	13 468 978 624	97.98	94.81	37.05	98.20	38	95.87
GY-H	88 204 618	13 174 359 352	97.99	94.89	36.78	99.38	37	96.44

样本名称Sample name	SNP数量SNP number	转换Transition	颠换Transversion	转换颠换比Ti/Tv	杂合SNP数Number of heterozygous SNPs	纯合SNP数Number of homozygous SNPs	杂合率Het-ratio (%)
GM	965 507	690 948	274 559	2.51	527 727	437 780	54.65
YY	990 492	707 374	283 118	2.49	666 029	324 463	67.24
GY-S	1 192 451	852 055	340 396	2.50	972 939	219 512	81.59
GY-H	1 197 004	856 131	340 873	2.51	961 753	235 251	80.34
总计Total	1 312 849	938 704	374 145	2.50	-	-	-

样本名称Sample name	SNP数量SNP number	转换Transition	颠换Transversion	转换颠换比Ti/Tv	杂合SNP数Number of heterozygous SNPs	纯合SNP数Number of homozygous SNPs	杂合率Het-ratio (%)
GM	965 507	690 948	274 559	2.51	527 727	437 780	54.65
YY	990 492	707 374	283 118	2.49	666 029	324 463	67.24
GY-S	1 192 451	852 055	340 396	2.50	972 939	219 512	81.59
GY-H	1 197 004	856 131	340 873	2.51	961 753	235 251	80.34
总计Total	1 312 849	938 704	374 145	2.50	-	-	-

基因编号Gene_ID	基因功能注释Annotation of gene function
Cp_zihui12720	DNA引导的RNA聚合酶 DNA-directed RNA polymerase
Cp_zihui07030	线粒体转录终止因子 Mitochodrial transcription termination factor
Cp_zihui06023	半乳糖基转移酶 Galactosyltransferase
Cp_zihui12764	2OG-Fe（Ⅱ）加氧酶家族 2OG-Fe（Ⅱ） oxygenase superfamily
Cp_zihui07021	GTPase激活蛋白 GTP-binding protein
Cp_zihui12712	NRT1/PTR蛋白家族 Protein NRT1/PTR FAMILY
Cp_zihui06951	蛋白质泛素连接酶 Putative E3 ubiquitin-protein ligase
Cp_zihui06022	2-烯醛还原酶 2-alkenal reductase （NADP（+）-dependent）
Cp_zihui12730	含U-box结构域的蛋白 U-box domain-containing protein
Cp_zihui12716	DeSI蛋白 DeSI-like protein
Cp_zihui05738	肌球蛋白7 Myosin-7
Cp_zihui07019	丝氨酸/苏氨酸蛋白激酶 Putative serine/threonine-protein kinase
Cp_zihui05736	肌球蛋白8 Myosin-8
Cp_zihui12718	NRT/PTR蛋白家族 Protein NRT1/PTR FAMILY
Cp_zihui07027	线粒体转录终止因子 Mitochodrial transcription termination factor-related protein
Cp_zihui06963	2OG-Fe（Ⅱ）加氧酶家族 2OG-Fe（Ⅱ） oxygenase superfamily
Cp_zihui06964	肌苷尿苷水解酶 Inosine-uridine preferring nucleoside hydrolase
Cp_zihui12725	木聚糖酶抑制剂N-末端 Xylanase inhibitor N-terminal
Cp_zihui06018	泛素自噬蛋白 Autophagy protein Atg8 ubiquitin like
Cp_zihui12734	肽基脯氨酰顺反异构酶CYP22 Peptidyl-prolyl cis-trans isomerase CYP22
Cp_zihui07025	线粒体转录终止因子 Mitochodrial transcription termination factor-related protein
Cp_zihui06953	叶绿体丙酮酸磷酸二激酶 Pyruvate， phosphate dikinase， chloroplastic
Cp_zihui16799	NPR1蛋白 NPR1 protein
Cp_zihui16893	Rbx 1a蛋白 RING-box protein 1a
Cp_zihui16892	类丝氨酸蛋白酶SBT1.8 Subtilisin-like protease SBT1.8
Cp_zihui05733	吲哚-3-丙酮酸单加氧酶YUCCA3 Indole-3-pyruvate monooxygenase YUCCA3
Cp_zihui07029	线粒体转录终止因子 Mitochodrial transcription termination factor
Cp_zihui07022	锌指结构域蛋白 Zinc finger CCCH domain-containing protein
Cp_zihui05696	28 kD 核糖核蛋白 28 kD ribonucleoprotein
Cp_zihui06020	S-酰基转移酶7 S-acyltransferase protein 7
Cp_zihui07024	AP2/ERF家族蛋白 AP2/ERF domain-containing protein
Cp_zihui05695	质体定位蛋白2 Plasmodesmata-located protein 2
Cp_zihui12731	磷脂酰肌醇激酶6 Phosphatidylinositol 4-phosphate 5-kinase 6
Cp_zihui12737	NADH脱氢酶 NADH dehydrogenase
Cp_zihui12732	TGA 6转录因子 Transcription factor TGA6
Cp_zihui12719	苯丙氨酸-tRNA连接酶 Phenylalanine--tRNA ligase
Cp_zihui12735	E3泛素蛋白连接酶 E3 ubiquitin-protein ligase