甜瓜幼果果皮颜色基因GR的精细定位

doi:10.3864/j.issn.0578-1752.2021.15.014

Abstract

Abstract:

【Objective】 The aim of this study was to explore the inheritance pattern of immature rind color of melon (Cucumis melo L.), to fine map target gene GR, and to deepen the understanding of rind color change during fruit growth, so as to provide a guidance for the improvement of melon color with molecular design breeding.【Method】 The dark-green rind line ‘MR-1’ (C. melo ssp. agrestis) and the light-green rind line ‘LGR’ (C. melo ssp. melo) were used as parents to construct the F₁ hybrid population, and the BC₁F₁backcross population was constructed from crossing by F₁ and ‘LGR’ for genetic analysis of immature rind color. By selecting 20 dark-green and light-green plants each in BC₁F₁population, the DNA was mixed, respectively, and the BSA-seq was operated for initial mapping. Based on the resequencing of two parents, the molecular markers with better specificity were developed in the initial region and recombinant individuals were identified and selected to verify and narrow the interval for fine mapping the GR gene. By sequencing of coding regions between two parents according to the gene annotation, the candidate gene and key variant site were determined. Moreover, the phenotype of immature and mature fruit in the BC₁F₁ backcross population was investigated and assessed by correlation analysis to explore the underlying mechanism of rind color transition in the fruit development.【Result】 According to the investigation, the phenotype of all F₁individual plants exhibited dark-green rind color. In addition, the immature rind color of BC₁F₁backcross population was found to be separated, and the ratio of the number of dark-green to light-green was approximately 1﹕1. As well as, the ratio of the number of dark-green to light-green in the F₂population was 3﹕1. These ratios corresponded to Mendel’s law of inheritance, indicating that the immature rind color of melon was a quality trait, controlled by a single nuclear gene GR, and the dark-green was dominant to light-green. Through BSA-seq, the gene was initially mapped to a 1.8 Mb interval on the long arm of chromosome 4. With developed molecular markers, 24 recombinant individuals were selected in expanded mapping population. The gene was further narrowed down to a region between markers 4-102 and 4-81 with a physical distance of 17.7 kb by genotype and phenotype verification of offspring, where were four predicted genes with latest annotation. Sequencing analysis revealed that a gene MELO3C003375 encoding GLKs transcription factor CmAPRR2 had several variations in ‘MR-1’ and ‘LGR’. Among them, there were three synonymous, a missense mutation, and a nonsense mutation. The nonsense mutation (G to T) appeared in the 856th base of the coding region led to premature translation termination and most of the Myb-DNA binding domain to be lost in ‘LGR’. Thus, the MELO3C003375 (CmAPRR2) was speculated to be the GR gene and the nonsense mutation was the key variation that affected the immature rind color of melon. It was found that there was a significant correlation between the rind color of immature fruit and mature fruit by investigating the phenotype of fruits in the BC₁F₁ backcross population.【Conclusion】 Immature rind color (dark green/light green) of melon was a quality trait and controlled by a single nuclear gene GR. By mapping, MELO3C003375 (CmAPRR2) was presumed to be the candidate gene that affected immature rind color.

Key words: melon, immature rind color, gene mapping, GR, MELO3C003375 (CmAPRR2)

XU XinYang,SHEN Jia,ZHANG YueJian,LI GuoJing,NIU XiaoWei,SHOU WeiSong. Fine Mapping of an Immature Rind Color Gene GR in Melon[J].Scientia Agricultura Sinica, 2021, 54(15): 3308-3319.

Figures/Tables 9

Fig. 1

Table 1

Fig. 2

Fig. 3

Table 2

Fig. 4

Table 3

Fig. 5

Table 4

Rind color of BC1F1 individuals"

单株 Individual	目测分型 Visual phenotype	测色仪分型 Colorimeter phenotype				单株 Individual	目测分型 Visual phenotype	测色仪分型 Colorimeter phenotype
单株 Individual	目测分型 Visual phenotype	L*	a*	b*	-a/b	单株 Individual	目测分型 Visual phenotype	L*	a*	b*	-a/b
1938-10	1	34.13	-9.27	12.92	0.72	1938-23	2	64.23	-21.15	37.73	0.56
1938-102	1	35.93	-11.70	15.61	0.75	1938-108	2	64.65	-21.53	39.58	0.54
1938-7	1	37.88	-11.34	15.67	0.72	1938-103	2	64.92	-18.34	35.51	0.52
1938-118	1	38.22	-11.56	15.74	0.73	1938-85	2	65.01	-21.73	38.89	0.56
1938-145	1	39.05	-14.92	19.32	0.77	1938-171	2	65.56	-16.07	30.12	0.53
1938-121	1	39.61	-11.60	16.06	0.72	1938-178	2	66.27	-19.51	36.34	0.54
1938-54	1	39.99	-12.87	18.36	0.70	1938-94	2	66.33	-20.65	37.11	0.56
1938-6	1	40.02	-13.92	19.04	0.73	1938-197	2	66.35	-20.05	37.66	0.53
1938-157	1	40.29	-14.03	18.26	0.77	1938-179	2	66.75	-18.38	35.02	0.52
1938-142	1	40.31	-14.97	20.42	0.73	1938-61	2	67.49	-18.07	33.77	0.54
1938-136	1	40.76	-12.21	16.60	0.74	1938-82	2	67.50	-20.62	37.68	0.55
1938-151	1	40.93	-13.66	19.46	0.70	1938-15	2	67.67	-21.07	41.99	0.50
1938-169	1	41.14	-16.18	22.67	0.71	1938-30	2	67.78	-20.14	38.48	0.52
1938-25	1	41.19	-12.37	16.92	0.73	1938-44	2	67.99	-18.63	34.39	0.54
1938-14	1	41.87	-12.74	17.96	0.71	1938-24	2	68.09	-18.93	35.43	0.53
1938-80	1	42.00	-13.50	18.71	0.72	1938-42	2	68.11	-14.18	26.98	0.53
1938-84	1	42.02	-13.71	18.85	0.73	1938-74	2	68.24	-16.08	30.06	0.53
1938-55	1	42.28	-16.38	23.00	0.71	1938-41	2	68.28	-19.11	36.31	0.53
1938-97	1	42.50	-12.92	18.75	0.69	1938-192	2	69.22	-18.21	35.16	0.52
1938-155	1	42.50	-13.65	19.51	0.70	1938-78	2	69.43	-16.80	34.09	0.49
1938-123	1	42.60	-15.64	22.26	0.70	1938-127	2	69.47	-18.10	35.94	0.50
1938-106	2	42.73	-15.78	32.13	0.49	1938-47	2	69.84	-12.30	25.56	0.48
1938-105	1	43.01	-14.05	20.31	0.69	1938-34	2	70.05	-13.82	27.42	0.50
1938-90	1	43.11	-15.87	22.53	0.70	1938-36	2	70.16	-16.87	31.90	0.53
1938-196	1	43.13	-15.91	23.06	0.69	1938-56	2	70.91	-18.35	36.30	0.51
1938-73	1	43.20	-14.87	20.70	0.72	1938-32	2	71.22	-20.39	39.66	0.51
1938-172	1	43.63	-15.79	22.55	0.70	1938-37	2	71.61	-14.19	29.57	0.48
1938-138	1	43.66	-19.06	27.68	0.69	1938-174	2	72.01	-17.03	33.74	0.50
1938-158	1	43.80	-15.26	21.35	0.71	1938-100	2	72.10	-16.69	33.75	0.49
1938-96	1	44.14	-13.62	19.23	0.71	1938-148	2	72.40	-12.86	26.55	0.48
1938-183	1	44.20	-15.36	21.77	0.71	1938-43	2	72.51	-16.45	33.17	0.50
1938-110	1	44.29	-14.86	20.62	0.72	1938-137	2	72.85	-17.16	33.69	0.51
1938-66	1	44.30	-14.96	21.47	0.70	1938-170	2	73.15	-10.46	22.55	0.46
1938-8	1	44.50	-15.71	22.95	0.68	1938-164	2	73.16	-15.30	30.24	0.51
1938-135	1	44.59	-16.82	23.88	0.70	1938-93	2	73.48	-10.44	23.49	0.44
1938-119	1	44.61	-14.32	20.77	0.69	1938-128	2	73.53	-10.25	23.35	0.44
1938-72	1	44.61	-15.18	21.38	0.71	1938-131	2	73.74	-12.46	26.94	0.46
1938-181	1	44.64	-17.28	24.91	0.69	1938-198	2	74.25	-15.37	30.34	0.51
单株 Individual	目测分型 Visual phenotype	测色仪分型 Colorimeter phenotype				单株 Individual	目测分型 Visual phenotype	测色仪分型 Colorimeter phenotype
单株 Individual	目测分型 Visual phenotype	L*	a*	b*	-a/b	单株 Individual	目测分型 Visual phenotype	L*	a*	b*	-a/b
1938-86	1	44.69	-16.33	23.36	0.70	1938-133	2	74.31	-7.57	23.46	0.32
1938-186	1	44.86	-17.29	24.84	0.70	1938-160	2	74.51	-13.13	27.28	0.48
1938-18	1	45.09	-17.55	25.70	0.68	1938-176	2	74.58	-11.32	23.60	0.48
1938-129	1	45.55	-14.07	19.89	0.71	1938-182	2	74.86	-14.14	30.47	0.46
1938-116	1	45.69	-19.19	29.01	0.66	1938-51	2	75.18	-9.40	22.19	0.42
1938-91	1	45.81	-14.98	21.89	0.68	1938-58	2	75.23	-14.90	32.67	0.46
1938-154	1	45.87	-17.03	24.69	0.69	1938-109	2	75.44	-10.67	22.89	0.47
1938-146	1	45.96	-15.47	22.17	0.70	1938-166	2	75.78	-8.28	24.49	0.34
1938-147	1	46.04	-17.91	26.64	0.67	1938-45	2	75.92	-9.62	21.11	0.46
1938-67	1	46.07	-16.66	24.57	0.68	1938-165	2	76.03	-10.21	22.82	0.45
1938-199	1	46.18	-16.44	24.74	0.66	1938-112	2	76.14	-9.10	21.58	0.42
1938-12	1	46.36	-13.68	20.22	0.68	1938-168	2	76.22	-9.99	23.75	0.42
1938-75	1	46.45	-14.91	21.76	0.69	1938-50	2	76.59	-8.39	23.53	0.36
1938-76	1	46.76	-19.53	27.56	0.71	1938-22	2	77.06	-7.11	22.34	0.32
1938-153	1	46.80	-13.74	19.54	0.70	1938-5	2	77.33	-9.11	22.33	0.41
1938-98	1	46.92	-17.90	26.62	0.67	1938-177	2	77.33	-13.14	27.97	0.47
1938-40	1	47.11	-20.92	30.50	0.69	1938-115	2	78.12	-9.06	23.98	0.38
1938-120	1	47.14	-17.81	27.06	0.66	1938-159	2	78.33	-7.92	21.01	0.38
1938-57	1	47.61	-13.86	20.00	0.69	1938-114	2	78.38	-9.95	22.76	0.44
1938-11	1	47.64	-17.65	26.57	0.66	1938-35	2	78.40	-8.03	23.03	0.35
1938-69	1	47.71	-14.40	20.78	0.69	1938-60	2	78.41	-8.91	23.92	0.37
1938-107	1	48.32	-14.43	21.45	0.67	1938-77	2	78.64	-9.13	22.56	0.40
1938-113	1	48.62	-16.57	24.84	0.67	1938-173	2	78.74	-8.24	22.42	0.37
1938-59	1	48.94	-17.18	25.16	0.68	1938-200	2	78.87	-14.35	30.49	0.47
1938-162	1	48.95	-16.55	24.53	0.67	1938-38	2	79.10	-9.19	22.90	0.40
1938-193	1	49.07	-14.29	20.99	0.68	1938-31	2	79.14	-7.07	21.17	0.33
1938-48	1	49.71	-16.18	23.58	0.69	1938-144	2	79.14	-9.61	23.88	0.40
1938-33	1	51.37	-12.38	19.50	0.63	1938-83	2	79.18	-5.58	20.69	0.27
1938-49	1	51.39	-16.94	25.05	0.68	1938-188	2	79.65	-7.15	19.66	0.36
1938-52	1	51.56	-16.89	24.72	0.68	1938-143	2	79.73	-8.08	21.52	0.38
1938-180	1	51.58	-19.16	30.58	0.63	1938-39	2	80.58	-6.52	21.68	0.30
1938-167	1	52.73	-18.01	28.87	0.62	1938-111	2	80.87	-5.44	21.39	0.25
1938-125	1	53.74	-19.25	33.86	0.57	1938-62	2	81.17	-5.93	18.66	0.32
1938-195	1	56.00	-21.92	35.41	0.62	1938-124	2	81.51	-6.67	18.92	0.35
1938-79	1	59.12	-19.87	39.01	0.51	1938-149	2	81.98	-7.08	25.33	0.28
1938-140	2	61.54	-21.20	38.29	0.55	1938-194	2	82.38	-4.25	20.43	0.21
1938-16	2	61.87	-22.45	39.16	0.57	1938-65	2	82.81	-6.49	26.53	0.24
1938-26	2	61.95	-23.03	40.14	0.57	1938-2	2	83.14	-4.57	21.21	0.22
1938-141	2	64.21	-19.76	37.03	0.53	1938-202	2	77.91	-6.22	33.89	0.18

Table 4

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组合 Cross	深绿皮植株 Dark green individual	浅绿皮植株 Light green individual	理论比 Expected ratio	Chi-square	P^a
P₁(MR-1)	10	0
P₂(LGR)	0	10
F₁(P₁×P₂)	25	0
F₁(P₂×P₁)	25	0
F₂(F₁?)	132	44	3﹕1	0.000	1.000
BC₁F₁(F₁×LGR)	98	89	1﹕1	0.433	0.510

引物名 Primer	正向引物 Forward primer (5'-3')	反向引物 Reverse primer (5'-3')
4-6	GGTGATCTAGGGCTTCTTTT	GGGCTTACCCTTGATTTAAC
4-15	CGGATAATGGGTTCTATGTG	CAATTCAATCCCCTCACTAC
4-78	TTTTCTTTTAACTTGGCCTG	TTTTTGGAAGAGGATACAACA
4-31	TGACATCAATAATGCCTCTTT	CTTGACGTAGGACAAATGGT
4-38	GAGGATTTGTTTGGCTTTTA	CATCTCTCATGTTGATGTCG
4-28	TAATCTAAGCTCCTTCGTGG	AGTTTATGAAGGCTTTGTGG
4-43	CTACGTGGTATCACAAGCAA	AGCCAAAGTGTAATGCAACT
4-58	ACGACAAATAAATCGGTGAT	TAGGAAATCAACCAAATGCT
4-102	TGTATTATCCTCCGGACAAC	AATTACCAACCAATCCAATG
4-81	TCGGTTAAAAAGAGCCATTA	GAAGATGATTATCGGATTGC
4-89	TGAGCAAAGGTTTACAACAA	GTAATTTCAAGATCGCCTTC
4-21	AACGGTACCAAACTAGGCTT	CTTATGTTGGGAATGTGACC

染色体 CHROM	位置 POS	参考碱基 REF	比对碱基 ALT	变异类型 Variant-classification	基因号 Gene_ID	参考氨基酸 REF (aa)	比对氨基酸 ALT (aa)
chr04	612438	T	G	错义突变 Missense_variant	MELO.jh030628.1	K	Q
chr04	612476	T	C	错义突变 Missense_variant	MELO.jh030628.1	N	S
chr04	612484	G	A	同义突变 Synonymous_variant	MELO.jh030628.1	A	A
chr04	612488	G	T	错义突变 Missense_variant	MELO.jh030628.1	T	K
chr04	612491	C	G	错义突变 Missense_variant	MELO.jh030628.1	R	P
chr04	612501	C	T	错义突变 Missense_variant	MELO.jh030628.1	E	Q
chr04	612505	A	G	同义突变 Synonymous_variant	MELO.jh030628.1	Y	S
chr04	612519	A	T	错义突变 Missense_variant	MELO.jh030628.1	I	I
chr04	613526	A	G	同义突变 Synonymous_variant	MELO3C003375	E	E
chr04	613558	G	C	错义突变 Missense_variant	MELO3C003375	R	P
chr04	614480	A	C	同义突变 Synonymous_variant	MELO3C003375	L	L
chr04	614898	T	C	同义突变 Synonymous_variant	MELO3C003375	G	G
chr04	615687	G	T	终止突变 Stop_gained	MELO3C003375	E	*
chr04	617619	A	G	错义突变 Missense_variant	MELO3C003375	Q	R
chr04	620196	T	G	错义突变 Missense_variant	MELO3C003376	L	R

Fine Mapping of an Immature Rind Color Gene GR in Melon

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