QTL Mapping and Candidate Genes Analysis of Irregular Fruit Cracking in Tomato

doi:10.16420/j.issn.0513-353x.2020-1032

Acta Horticulturae Sinica ›› 2021, Vol. 48 ›› Issue (7): 1329-1339.doi: 10.16420/j.issn.0513-353x.2020-1032

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QTL Mapping and Candidate Genes Analysis of Irregular Fruit Cracking in Tomato

CHEN Bin, WU Zhen, WEN Junqin, LIN Haowei, YU Lu, XUE Lingzi, ZHOU Rong, JIANG Fangling^*()

College of Horticulture,Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China,Ministry of Agriculture and Rural Affairs,Nanjing Agricultural University,Nanjing 210095,China

Received:2021-02-07 Revised:2021-05-25 Online:2021-07-25 Published:2021-08-10
Contact: JIANG Fangling E-mail:jfl@njau.edu.cn

Abstract

Abstract:

In order to excavate key regulatory genes for irregular fruit cracking in tomato,the F₁ and F₂ offspring were obtained by crossing the cracking-susceptible（CS）germplasm accession‘S189’and the cracking-resistant（CR）germplasm accession‘R91’and subsequent self-crossing. QTL-seq approach was applied to identify candidate QTLs. Genomic DNA of 20 CS and 20 CR F₂ individuals were evenly mixed as CS-pool and CR-pool,respectively. A total of two QTLs that regulated irregular fruit cracking in tomato were detected,which were physically located in the region of 38.75-42.14 Mb on chromosome 2 and the region of 49.07-49.48 Mb on chromosome 5. The two QTLs were temporarily designated as qCR2 and qCR5. In view of the fact that there were only two genes in the region of qCR5,the differences at gene expression levels were analyzed using the mature fruit pericarps from the parents. However,both the results showed no significant differences between the parents. Considering that the region of qCR2 was relatively large,in order to quickly and effectively mine candidate genes,the linkage map of chromosome 2 was constructed using 43 polymorphic markers. Afterwards,traditional QTL analysis was carried out based on the fruit cracking rate of F₂ population. A major QTL was detected between the polymorphic markers sli2734 and Bin3371,whose LOD score was 3.05 and contribution rate was 7.05%. The corresponding physical location of the major QTL was coincided with the qCR2’s region. According to the results from both QTL-seq and traditional QTL analysis,the candidate region was delimited between 39.55-39.94 Mb,eventually designated as qCR2.1. There were a total of 53 genes in qCR2.1’s region. Accordingly,the mature fruit pericarps from the parents were used to analyze the differences at gene expression levels and thus three genes with significantly different expression levels were obtained,namely Solyc02g072400,Solyc02g072470 and Solyc02g076780. Among them,the expression levels of Solyc02g076780 between the parents were extremely significantly different. Solyc02g076780 played a role in ethylene regulation,which could be a key candidate gene for irregular fruit cracking in tomato.

Key words: tomato, irregular fruit cracking, QTL mapping, candidate gene

CLC Number:

S641.2

CHEN Bin, WU Zhen, WEN Junqin, LIN Haowei, YU Lu, XUE Lingzi, ZHOU Rong, JIANG Fangling. QTL Mapping and Candidate Genes Analysis of Irregular Fruit Cracking in Tomato[J]. Acta Horticulturae Sinica, 2021, 48(7): 1329-1339.

Figures/Tables 7

Fig.1 Fruit traits of parents

Table 1 Primer sequences of partial markers

标记类型	标记	正向引物（5′-3′）	反向引物（5′-3′）
Protocol	Marker	Forward primer	Reverse primer
SSR	SSR50	CCGTGACCCTCTTTACAAGC	TTGCTTTCTTCTTCGCCATT
	SSR287	GCATCCCAAACAATCCAATC	TCCACTTTCAAGATCAGAGCAA
	TES373	GCCAATGGCTTTGTTGAAGGT	ATGGTGACTTTGCCCTTGTC
	TES992	GATGGACTGGCTCTGGCTCTA	TCACCATCACTGCTTCCATC
InDel	C02M36734	GACAAATATCATTCGTTTTAATG	CCAAAACACCAAATAATTACTAA
	C02M52141	TTCTTATGTCCTCCGAACAAC	GGACTACACCCTACTTAGGCTA
	Bin3361	CAGGGGAACTCCAAATTTCA	CACATGGTATCAAAGCACGG
	Bin3371	GAAGTTGACACAATCCCGCT	TCGAAATCAGATCCAACTGC
	sli2734	GGTAGGGATCTTGAGCATGG	GGAGCCAGAGGGATCAAAAG
	sli2763	AAGGTCTCTCCCTTTGAGCTG	TTGATCATGAGGGTAGCCTTG

Fig.2 Frequency distribution histogram of fruit cracking rate in F2 population of tomato

Fig. 3 Distribution of Δ（SNP-index）（A）,WB-SNP-index（B）and MB-SNP-index（C）in the whole genome The scattered points in the figure represent the calculated values of ΔSNP-index and SNP-index;The black curve represents the corresponding fitting value;The red dotted line represents 99% threshold line set by LOESS.

Fig.4 Polymorphic marker（sli2747）strip chart

Fig.5 QTL mapping on tomato chromosome 2

Fig. 6 Significantly differentially expressed genes * P < 0.05;** P < 0.01;*** P < 0.001.

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QTL Mapping and Candidate Genes Analysis of Irregular Fruit Cracking in Tomato

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