Allele-specific Imbalance Analysis and Related Molecular Marker Development in Rosa chinensis‘Old Blush’

doi:10.16420/j.issn.0513-353x.2023-0970

Acta Horticulturae Sinica ›› 2025, Vol. 52 ›› Issue (2): 365-379.doi: 10.16420/j.issn.0513-353x.2023-0970

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

Allele-specific Imbalance Analysis and Related Molecular Marker Development in Rosa chinensis‘Old Blush’

YAN Xu, LI Yue, FU Xiaopeng, NING Guogui, LIANG Mei^*()

National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops，Huazhong Agricultural University，Wuhan 430070，China

Received:2024-09-15 Revised:2024-12-23 Online:2025-02-25 Published:2025-02-23
Contact: LIANG Mei

Abstract

Abstract:

In this study，a comprehensive comparative analysis of the two haplotype genomes of Rosa chinensis‘Old Blush’were conducted using RcOB_hap1 and RcOB_hap2. The allele-specific imbalance analysis was conducted by bioinformatics methods，and the corresponding molecular markers were developed，providing a basis for the breeding of the cultivated rose. The results showed that two haplotype genomes had a good collinearity relationship，but the assembly integrity of RcOB_hap2 is better than RcOB_hap1. The heterozygosity of‘Old Blush’rose was 3.48%，containing a large number of single nucleotide polymorphisms，fragment insertions or deletions and chromosomal variations. A total of 1 157 allele-specific protein function genes and 720 allele-specific expression genes were identified in the whole genome. GO annotation and KEGG enrichment analyses of all imbalanced alleles showed that they were mainly involved in the processes of metabolism and synthesis，plant growth and development，and environmental adaptation. Imbalanced alleles AP2，MBY4 and DSC1 were selected for developing molecular markers for floral organ development，aroma synthesis and immune response，respectively. Based on the results of the molecular markers within 183 materials found that the Hap2 AP2 allele had incomplete protein function and was strongly selected in cultivated roses with double flower；For the MBY4，its Hap2 allele showed lower expression and was adopted by most cultivated roses，that might lead cultivated rose emitting less benzenoid volatile；DSC1’s Hap1 allele had lower expression and possible defect protein function，but it was selected in cultivated varieties，that might result in a reduction of the disease resistance in cultivated roses.

Key words: rose, allele-specific imbalance, allelic protein function differences, allele-specific expression, molecular marker

YAN Xu, LI Yue, FU Xiaopeng, NING Guogui, LIANG Mei. Allele-specific Imbalance Analysis and Related Molecular Marker Development in Rosa chinensis‘Old Blush’[J]. Acta Horticulturae Sinica, 2025, 52(2): 365-379.

Figures/Tables 9

References 53

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引物 Primer	正引物序列（5′-3′） Forward primer	反引物序列（5′-3′） Reverse primer	片段大小/bp Fragment size	基因ID Gene ID
AP2	TCATCTATGAAAGAATTTGGAG	GAAGGAATGCGACTGTTAGG	Hap1：962 Hap2：807	Rc3g0243000 Rc3g0468481
MYB4	TAGGACTCAAGT TACCACAA	TCGTGAGGTACATTATCATCTA	Hap1：240 Hap2：430	Rc7g0018900 Rc7g0178681
DSC1	CGTGAGGTACAT TATCATCTA	AAGATGACTGGACCAGAGCAA	Hap1：599 Hap2：1051	Rc3g0384800 Rc3g0451671

引物 Primer	正引物序列（5′-3′） Forward primer	反引物序列（5′-3′） Reverse primer	片段大小/bp Fragment size	基因ID Gene ID
AP2	TCATCTATGAAAGAATTTGGAG	GAAGGAATGCGACTGTTAGG	Hap1：962 Hap2：807	Rc3g0243000 Rc3g0468481
MYB4	TAGGACTCAAGT TACCACAA	TCGTGAGGTACATTATCATCTA	Hap1：240 Hap2：430	Rc7g0018900 Rc7g0178681
DSC1	CGTGAGGTACAT TATCATCTA	AAGATGACTGGACCAGAGCAA	Hap1：599 Hap2：1051	Rc3g0384800 Rc3g0451671

基因 Gene	SNP编号 SNP ID	Hap1型读长数 Hap1-type read number	Hap2型读长数 Hap2-type read number	变化倍数的log₂值 log₂fold change	ASE基因（是/否） ASE gene (yes/no)	P值 P-value	基因注释 Annotation
Rc1g0350201	Chr01_43344427	0	131	-10.17	是 Yes	8.28e^-108	未知蛋白 Unknown protein
	Chr01_43344491	0	149
	Chr01_43344521	0	136
	Chr01_43344550	0	158
	小计Subtotal	0	574
Rc2g0129651	Chr02_45318393	31	53	-0.83	否 No	1.15e^-4	未知蛋白 Unknown protein
	Chr02_45318518	30	53
	Chr02_45318530	30	56
	Chr02_45318549	30	53
	小计Subtotal	121	215
Rc3g0468121	Chr03_14202662	86	13	2.83	是 Yes	1.70e^-47	磷酸酶 Protein phosphatase
	Chr03_14202709	81	13
	Chr03_14202963	69	10
	Chr03_14203072	75	8
	Chr03_14204073	84	11
	小计Subtotal	395	55
Rc5g0077891	Chr05_83740197	173	133	0.35	否 No	2.74e^-4	未知蛋白 Unknown protein
Rc5g0077891	Chr05_83740290	132	107	0.35	否 No	2.74e^-4	未知蛋白 Unknown protein
	小计Subtotal	305	240

基因 Gene	SNP编号 SNP ID	Hap1型读长数 Hap1-type read number	Hap2型读长数 Hap2-type read number	变化倍数的log₂值 log₂fold change	ASE基因（是/否） ASE gene (yes/no)	P值 P-value	基因注释 Annotation
Rc1g0350201	Chr01_43344427	0	131	-10.17	是 Yes	8.28e^-108	未知蛋白 Unknown protein
	Chr01_43344491	0	149
	Chr01_43344521	0	136
	Chr01_43344550	0	158
	小计Subtotal	0	574
Rc2g0129651	Chr02_45318393	31	53	-0.83	否 No	1.15e^-4	未知蛋白 Unknown protein
	Chr02_45318518	30	53
	Chr02_45318530	30	56
	Chr02_45318549	30	53
	小计Subtotal	121	215
Rc3g0468121	Chr03_14202662	86	13	2.83	是 Yes	1.70e^-47	磷酸酶 Protein phosphatase
	Chr03_14202709	81	13
	Chr03_14202963	69	10
	Chr03_14203072	75	8
	Chr03_14204073	84	11
	小计Subtotal	395	55
Rc5g0077891	Chr05_83740197	173	133	0.35	否 No	2.74e^-4	未知蛋白 Unknown protein
Rc5g0077891	Chr05_83740290	132	107	0.35	否 No	2.74e^-4	未知蛋白 Unknown protein
	小计Subtotal	305	240

基因 Gene	等位基因比较 Allele comparison		基因型频率 Frequency of different genotypes
基因 Gene	基因表达（有/无差异） Gene expression（DIF./No DIF.）	蛋白功能（有/无差异） Protein function（DIF./No DIF.）	36份野生种 36 wild species	147份栽培种 147 cultivated varieties
AP2	有差异（茎和刺：Hap1 < Hap2） DIF.（Hap1 < Hap2 in stem & prickle）	有差异（Hap2型：提前终止） DIF.（Hap2-type：Premature）	Hap2: 8 Hap1&2: 6 Hap2&3: 6 Hap3: 9 No band: 7	Hap2: 45 Hap1&2: 18 Hap2&3: 70 Hap3: 5 Hap1&3: 6 No band: 3
MYB4	有差异（茎和雌蕊：Hap1 < Hap2） DIF.（Hap1 < Hap2 in stem & pistil）	无差异 No DIF.	Hap1: 17 Hap2: 1 Hap1&2: 11 No band: 7	Hap1: 94 Hap2: 5 Hap1&2: 47 No band: 1
DSC1	有差异（所有组织：Hap1 < Hap2） DIF.（Hap1 < Hap2 in all tissues）	有差异（Hap1型：移码）（Hap1-type：Frame shift）	Hap1: 3 Hap2: 3 Hap1&2: 6 No band: 24	Hap1: 83 Hap2: 5 Hap1&2: 30 No band: 29

Allele-specific Imbalance Analysis and Related Molecular Marker Development in Rosa chinensis‘Old Blush’

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