Fine-Mapping and KASP Marker Development for the Gene Underlying Green Fruit in Eggplant

doi:10.16420/j.issn.0513-353x.2023-0567

Acta Horticulturae Sinica ›› 2024, Vol. 51 ›› Issue (9): 2008-2018.doi: 10.16420/j.issn.0513-353x.2023-0567

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

Fine-Mapping and KASP Marker Development for the Gene Underlying Green Fruit in Eggplant

XIA Zhilei¹, YU Bingxin¹, YANG Meng¹, LIAN Zilin¹, GUAN Lilan², HE Yichao², YAN Shuangshuang¹, CAO Bihao¹, QIU Zhengkun¹^,^*()

¹ Key Laboratory of Biology and Genetic Improvement of Horticultural Crops，Ministry of Agriculture and Rural Affairs，College of Horticulture，South China Agricultural University，Guangzhou 510642，China
² Guangdong Enping Agricultural Technology Extension Center，Jiangmen，Guangdong 529499，China

Received:2024-05-17 Revised:2024-07-16 Online:2024-09-25 Published:2024-09-19
Contact: QIU Zhengkun

Abstract

Abstract:

An F₂ population developing by a white fruit eggplant line E802 and a green fruit eggplant line NY was used for the genetic analysis of the gene underlying green fruit color. The segregation ratio of green fruit and white in the 304 individuals in the F₂ population was 3︰1，indicating that the green phenotype of NY is controlled by a single dominant locus. Combing with the BSA-seq and linkage-based QTL mapping，the gene underlying green fruit color of eggplant was fine-mapped into 683.4 kb interval on chromosome 8 using F₂ and the F_2:3population. The genetic distance of this locus is 0.17 cM. Among the 46 genes in the interval，SmAPRR2 was the best candidate gene. The 5.27 kb deletion was detected in the E802，resulting the SmAPRR2 lacking the exon 7 to 11. In addition，a tightly linked to SmAPRR2 KASP marker，22QP296，was development. The accuracies of 22QP296 for predicting the skin color（green or white）in the F₂ population and the 194 cultivars were 100% and 94.85%，respectively，indicating that this KASP marker can be used in molecular marker-assisted selection in eggplant breeding.

Key words: eggplant, fruit color, gene mapping, KASP marker, green fruit gene, APRR2

XIA Zhilei, YU Bingxin, YANG Meng, LIAN Zilin, GUAN Lilan, HE Yichao, YAN Shuangshuang, CAO Bihao, QIU Zhengkun. Fine-Mapping and KASP Marker Development for the Gene Underlying Green Fruit in Eggplant[J]. Acta Horticulturae Sinica, 2024, 51(9): 2008-2018.

Figures/Tables 6

References 34

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引物名称 Primer name	引物序列（5′-3′） Primer sequence
22QP296	F_P1：GAAGGTGACCAAGTTCATGCTAAGGACAGTCTAATCACCACTCTG
	F_P2：GAAGGTCGGAGTCAACGGATTAAGGACAGTCTAATCACCACTCTA
	R：GCATTTGGGAGACATGCATGAATA
22QP299	F_P1：GAAGGTGACCAAGTTCATGCTAATTGCCGTTCAAAGTGTACGTAC
	F_P2：GAAGGTCGGAGTCAACGGATTAATTGCCGTTCAAAGTGTACGTAT
	R：AAACTGGTCGAACAATAAAGGACG
22QP302	F_P1：GAAGGTGACCAAGTTCATGCTAGGAATATCTTCTCTCGTCTCGAC
	F_P2：GAAGGTCGGAGTCAACGGATTAGGAATATCTTCTCTCGTCTCGAT
	R：AATTGTACAACATACCCTCCAGCA
22QP308	F_P1：GAAGGTGACCAAGTTCATGCTGGGAAGTGCATTCTACTTTTCATACA
	F_P2：GAAGGTCGGAGTCAACGGATTGGGAAGTGCATTCTACTTTTCATACT
	R：GTTGCTCCGCTCTTAATCAAAAGT
22QP311	F_P1：GAAGGTGACCAAGTTCATGCTACATAATTCCTCGATTAAATGTAGGGAATA
	F_P2：GAAGGTCGGAGTCAACGGATTACATAATTCCTCGATTAAATGTAGGGAATG
	R：TCTTTGTCACGTCATACTAATTGCA
22QP314	F_P1：GAAGGTGACCAAGTTCATGCTTGTTTGGTATGAATATAAAGGACCACTAAT
	F_P2：GAAGGTCGGAGTCAACGGATTTGTTTGGTATGAATATAAAGGACCACTAAC
	R：TGAATTCATCACGGACACAATTGT
22QP317	F_P1：GAAGGTGACCAAGTTCATGCTGGGAGAACGACACAAGCTGA
	F_P2：GAAGGTCGGAGTCAACGGATTGGGAGAACGACACAAGCTGT
	R：ACCTGAATGCACATGATAGTGACT
22QP320	F_P1：GAAGGTGACCAAGTTCATGCTTGAGTAAACTAACTTCTAGTCTCTCTG
	F_P2：GAAGGTCGGAGTCAACGGATTTGAGTAAACTAACTTCTAGTCTCTCTA
	R：TGGCACACAAATTAATACTCCAGA
22QP323	F_P1：GAAGGTGACCAAGTTCATGCTTGTTGTATATCGAGCATTGGTTGATTAA
	F_P2：GAAGGTCGGAGTCAACGGATTTGTTGTATATCGAGCATTGGTTGATTAG
	R：GAACTTTAAAACACAGTCAGCGGT
22QP326	F_P1：GAAGGTGACCAAGTTCATGCTCTTACTCTACGTCCCAAAGTCCCT
	F_P2：GAAGGTCGGAGTCAACGGATTCTTACTCTACGTCCCAAAGTCCCC
	R：ACAAAACCGCTAAATCTACCCCTA
22QP437	F_P1：GAAGGTGACCAAGTTCATGCTATTACTGAGTTGCTCATCCATGAA
	F_P2：GAAGGTCGGAGTCAACGGATTATTACTGAGTTGCTCATCCATGAT
	R：ACCTTCACCATCTTGTACTTGAGA
22QP539	F_P1：GAAGGTGACCAAGTTCATGCTACTCTTCAGTGCTCAGTTCCATTAT
	F_P2：GAAGGTCGGAGTCAACGGATTACTCTTCAGTGCTCAGTTCCATTAG
	R：AACAAAAACCATTGCCAGAGTGAG
22QP542	F_P1：GAAGGTGACCAAGTTCATGCTGGTGTTAAGATCAATATAATTAGGCTCCAAT
	F_P2：GAAGGTCGGAGTCAACGGATTGGTGTTAAGATCAATATAATTAGGCTCCAAA
	R：GGAAAAGTGGAGAAAAGCACGAAA
22QP545	F_P1：GAAGGTGACCAAGTTCATGCTAGAATATCTGATTCGAGTTTAATTAAAACCA
	F_P2：GAAGGTCGGAGTCAACGGATTAGAATATCTGATTCGAGTTTAATTAAAACCT
	R：TTCCATCACTTGTTGTTAGCTTCT
22QP548	F_P1：GAAGGTGACCAAGTTCATGCTTCTTACTTGTTAATTACGTCTTTCTATTCAG
	F_P2：GAAGGTCGGAGTCAACGGATTTCTTACTTGTTAATTACGTCTTTCTATTCAA
	R：TGGATGGAATTTCTTTGTCCAAAA
23QP26	F_P1：GAAGGTGACCAAGTTCATGCTATTTATCCATATTTATCACGAGTTCATATAAG
	F_P2：GAAGGTCGGAGTCAACGGATTATTTATCCATATTTATCACGAGTTCATATAAA
	R：GCCGAGTTCAAACTTCAAAGTACT
23QP29	F_P1：GAAGGTGACCAAGTTCATGCTTCCAGGAGGGAATGTTTTCGC
	F_P2：GAAGGTCGGAGTCAACGGATTTCCAGGAGGGAATGTTTTCGT
	R：TTAGTCGGAAGCCTCTCAATTTCA
23QP32	F_P1：GAAGGTGACCAAGTTCATGCTCTTTGCCTCCTTTTGTTGTTTCTG
	F_P2：GAAGGTCGGAGTCAACGGATTCTTTGCCTCCTTTTGTTGTTTCTA
	R：GGTCATACTCTACCGTCCTTTTGT

引物名称 Primer name	引物序列（5′-3′） Primer sequence
22QP296	F_P1：GAAGGTGACCAAGTTCATGCTAAGGACAGTCTAATCACCACTCTG
	F_P2：GAAGGTCGGAGTCAACGGATTAAGGACAGTCTAATCACCACTCTA
	R：GCATTTGGGAGACATGCATGAATA
22QP299	F_P1：GAAGGTGACCAAGTTCATGCTAATTGCCGTTCAAAGTGTACGTAC
	F_P2：GAAGGTCGGAGTCAACGGATTAATTGCCGTTCAAAGTGTACGTAT
	R：AAACTGGTCGAACAATAAAGGACG
22QP302	F_P1：GAAGGTGACCAAGTTCATGCTAGGAATATCTTCTCTCGTCTCGAC
	F_P2：GAAGGTCGGAGTCAACGGATTAGGAATATCTTCTCTCGTCTCGAT
	R：AATTGTACAACATACCCTCCAGCA
22QP308	F_P1：GAAGGTGACCAAGTTCATGCTGGGAAGTGCATTCTACTTTTCATACA
	F_P2：GAAGGTCGGAGTCAACGGATTGGGAAGTGCATTCTACTTTTCATACT
	R：GTTGCTCCGCTCTTAATCAAAAGT
22QP311	F_P1：GAAGGTGACCAAGTTCATGCTACATAATTCCTCGATTAAATGTAGGGAATA
	F_P2：GAAGGTCGGAGTCAACGGATTACATAATTCCTCGATTAAATGTAGGGAATG
	R：TCTTTGTCACGTCATACTAATTGCA
22QP314	F_P1：GAAGGTGACCAAGTTCATGCTTGTTTGGTATGAATATAAAGGACCACTAAT
	F_P2：GAAGGTCGGAGTCAACGGATTTGTTTGGTATGAATATAAAGGACCACTAAC
	R：TGAATTCATCACGGACACAATTGT
22QP317	F_P1：GAAGGTGACCAAGTTCATGCTGGGAGAACGACACAAGCTGA
	F_P2：GAAGGTCGGAGTCAACGGATTGGGAGAACGACACAAGCTGT
	R：ACCTGAATGCACATGATAGTGACT
22QP320	F_P1：GAAGGTGACCAAGTTCATGCTTGAGTAAACTAACTTCTAGTCTCTCTG
	F_P2：GAAGGTCGGAGTCAACGGATTTGAGTAAACTAACTTCTAGTCTCTCTA
	R：TGGCACACAAATTAATACTCCAGA
22QP323	F_P1：GAAGGTGACCAAGTTCATGCTTGTTGTATATCGAGCATTGGTTGATTAA
	F_P2：GAAGGTCGGAGTCAACGGATTTGTTGTATATCGAGCATTGGTTGATTAG
	R：GAACTTTAAAACACAGTCAGCGGT
22QP326	F_P1：GAAGGTGACCAAGTTCATGCTCTTACTCTACGTCCCAAAGTCCCT
	F_P2：GAAGGTCGGAGTCAACGGATTCTTACTCTACGTCCCAAAGTCCCC
	R：ACAAAACCGCTAAATCTACCCCTA
22QP437	F_P1：GAAGGTGACCAAGTTCATGCTATTACTGAGTTGCTCATCCATGAA
	F_P2：GAAGGTCGGAGTCAACGGATTATTACTGAGTTGCTCATCCATGAT
	R：ACCTTCACCATCTTGTACTTGAGA
22QP539	F_P1：GAAGGTGACCAAGTTCATGCTACTCTTCAGTGCTCAGTTCCATTAT
	F_P2：GAAGGTCGGAGTCAACGGATTACTCTTCAGTGCTCAGTTCCATTAG
	R：AACAAAAACCATTGCCAGAGTGAG
22QP542	F_P1：GAAGGTGACCAAGTTCATGCTGGTGTTAAGATCAATATAATTAGGCTCCAAT
	F_P2：GAAGGTCGGAGTCAACGGATTGGTGTTAAGATCAATATAATTAGGCTCCAAA
	R：GGAAAAGTGGAGAAAAGCACGAAA
22QP545	F_P1：GAAGGTGACCAAGTTCATGCTAGAATATCTGATTCGAGTTTAATTAAAACCA
	F_P2：GAAGGTCGGAGTCAACGGATTAGAATATCTGATTCGAGTTTAATTAAAACCT
	R：TTCCATCACTTGTTGTTAGCTTCT
22QP548	F_P1：GAAGGTGACCAAGTTCATGCTTCTTACTTGTTAATTACGTCTTTCTATTCAG
	F_P2：GAAGGTCGGAGTCAACGGATTTCTTACTTGTTAATTACGTCTTTCTATTCAA
	R：TGGATGGAATTTCTTTGTCCAAAA
23QP26	F_P1：GAAGGTGACCAAGTTCATGCTATTTATCCATATTTATCACGAGTTCATATAAG
	F_P2：GAAGGTCGGAGTCAACGGATTATTTATCCATATTTATCACGAGTTCATATAAA
	R：GCCGAGTTCAAACTTCAAAGTACT
23QP29	F_P1：GAAGGTGACCAAGTTCATGCTTCCAGGAGGGAATGTTTTCGC
	F_P2：GAAGGTCGGAGTCAACGGATTTCCAGGAGGGAATGTTTTCGT
	R：TTAGTCGGAAGCCTCTCAATTTCA
23QP32	F_P1：GAAGGTGACCAAGTTCATGCTCTTTGCCTCCTTTTGTTGTTTCTG
	F_P2：GAAGGTCGGAGTCAACGGATTCTTTGCCTCCTTTTGTTGTTTCTA
	R：GGTCATACTCTACCGTCCTTTTGT

表型 Phenotype	基因型 Genotype	一致 Correct	不一致 Incorrect	正确率/% Accuracy rate
绿茄 Green fruit	杂合Heterozygous	50	1	94.85
	NY	131	5	94.85
白茄 White fruit	E802	3	4

表型 Phenotype	基因型 Genotype	一致 Correct	不一致 Incorrect	正确率/% Accuracy rate
绿茄 Green fruit	杂合Heterozygous	50	1	94.85
	NY	131	5	94.85
白茄 White fruit	E802	3	4

Fine-Mapping and KASP Marker Development for the Gene Underlying Green Fruit in Eggplant

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