Gene Mapping of Kale White Leaves Based on Whole Genome Re-sequencing of Extreme Mixed Pool（BSA）

doi:10.13560/j.cnki.biotech.bull.1985.2023-0275

Abstract

Abstract:

This study is aimed to screen for key genes and loci associated with white leaf formation in kale（Brassica oleracea L. var. acephala DC）and the genetic patterns of heart leaf color traits. The kale red-leaf parent WR, the white-leaf parent WB and their constructed F₂ segregating populations were used as test materials. Twenty red-leaf and white-leaf plants were selected from the F₂ population, and two DNA mixing pools were constructed. Whole genome sequencing to offspring mixing pool and parents at 50x and 20x cover depth was conducted respectively, and the association interval of white leaf traits was located and candidate genes were predicted according to the gene annotation information. The results showed that re-sequencing 3 987 718 single nucleic acid polymorphism（SNP）markers were obtained via re-sequencing, 8 significant association intervals on chromosomes 2,3, and 9 were obtained, and 8 candidate genes（Bol030253, Bol029431, Bol012077, Bol007709, Bol030318, Bol030235, Bol030286, and Bol005195）were obtained based on gene annotation and functional analysis. Identifying eight genes as candidate genes for white kale leaves may play an important role in the color formation of kale leaves.

Key words: kale, whole genome sequencing, BSA, white leaf, gene mapping

WANG Teng-hui, GE Wen-dong, LUO Ya-fang, FAN Zhen-yu, WANG Yu-shu. Gene Mapping of Kale White Leaves Based on Whole Genome Re-sequencing of Extreme Mixed Pool（BSA）[J]. Biotechnology Bulletin, 2023, 39(9): 176-182.

Figures/Tables 7

References 28

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群体 Group	总株数 Total plants	红叶株数 No. of red-leaf plants	白叶株数 No. of white-leaf plants	红叶∶白叶 Red leaf∶White leaf	卡方值 χ²	检验值 χ²_0.05
WR	20	20	0	-	-	-
WB	20	0	20	-	-	-
F₁	20	20	0	-	-	-
F₂	1 300	982	318	3.09∶1	0.20	3.84

群体 Group	总株数 Total plants	红叶株数 No. of red-leaf plants	白叶株数 No. of white-leaf plants	红叶∶白叶 Red leaf∶White leaf	卡方值 χ²	检验值 χ²_0.05
WR	20	20	0	-	-	-
WB	20	0	20	-	-	-
F₁	20	20	0	-	-	-
F₂	1 300	982	318	3.09∶1	0.20	3.84

样品 Sample	Clean reads数 Number of clean reads	比对reads数 Mapped reads	参考基因组比对 Map ratio/%	平均覆盖深度 Average cover depth	基因组覆盖度 Coverage/%	碱基数质量值大于Q20/%
W12	122 570 282	117 542 515	95.90	29.03	88.05	98.35
W06	156 059 918	148 403 662	95.09	35.68	88.38	98.17
L-bulk	370 780 056	352 633 985	95.11	81.94	91.05	98.19
B-bulk	324 884 700	307 268 196	94.58	73.98	91.12	97.81

样品 Sample	Clean reads数 Number of clean reads	比对reads数 Mapped reads	参考基因组比对 Map ratio/%	平均覆盖深度 Average cover depth	基因组覆盖度 Coverage/%	碱基数质量值大于Q20/%
W12	122 570 282	117 542 515	95.90	29.03	88.05	98.35
W06	156 059 918	148 403 662	95.09	35.68	88.38	98.17
L-bulk	370 780 056	352 633 985	95.11	81.94	91.05	98.19
B-bulk	324 884 700	307 268 196	94.58	73.98	91.12	97.81

变异位点信息 Variation sites information	WR	WB	R-bulk	B-bulk
基因区间 Intergenic region	525 758	529 072	555 294	555 413
非同义突变 Non-synonymous	266 962	270 929	283 962	283 910
同义突变 Synonymous	150 618	152 757	159 396	159 535
起始密码子丢失 Start lost	611	628	672	668
终止密码子丢失 Stop_lost	6 645	6 703	7 028	7 075
终止密码子获得 Stop_Gained	13 829	13 994	14 600	14 596
5'非翻译区 UTR_5_Prime	489	484	511	512
SNP总数 SNP total	964 912	979 644	1 021 463	1 021 699