Cotton Science

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Genome-wide association study of cotton lint percentage and boll weight

Du Xiao, Long Yilei, Tan Yanping, Li Lili, Wang Yin, Jin Shen, Yang Yinan, Ai Xiantao

Cotton Science, 2024, 36(6): 455-473. DOI: 10.11963/cs20240018

性状 Trait	环境 Environment	最小值 Minimum	最大值 Maximum	平均 Mean	SD	偏度 Kurtosis	峰度 Skewness	CV/%	H²/%
LP/%	E1	18.45	57.16	39.82	4.70	-0.47	1.36	11.82	92.81
	E2	26.82	52.15	40.02	4.11	-0.35	0.38	10.26
	E3	28.55	48.54	40.98	3.60	-0.65	0.29	8.80
	E4	28.53	48.97	40.69	3.48	-0.42	0.10	8.55
	E5	27.46	58.54	40.55	3.98	-0.24	1.22	9.82
	BLUP	30.05	47.33	40.34	2.88	-0.60	0.44	7.14
BW/g	E1	3.96	8.78	6.33	0.83	0.05	0.22	13.04	86.67
	E2	3.47	8.58	6.04	0.89	0.14	0.22	14.79
	E3	3.37	8.32	6.10	0.80	-0.13	0.14	13.15
	E4	4.01	8.16	6.11	0.74	0.07	-0.22	12.08
	E5	2.91	7.88	6.06	0.73	-0.37	0.57	12.10
	BLUP	4.95	7.20	6.13	0.40	-0.20	0.13	6.60

Table 2 Statistical analysis of lint percentage and boll weight

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Table 1 The origins of 300 cotton germplasm materials
Fig. 1 Correlation between cotton lint percentage and boll weight under different environments *, **, ***: significance at the 0.05, 0.01, and 0.001 probability level, respectively.
Fig. 2 Population structure, phylogeny, principal component analysis and linkage disequilibrium decay analysis of 300 upland cotton materials A: Optimal number of subgroups by cross-validation; B: Phylogenetic tree; C: Population structure analysis with K = 6; D: PCA analysis; E: Linkage disequilibrium decay.
Fig. 3 Position of QTL related to cotton lint percentage and boll weight on chromosomes The numbers on the left side of the chromosomes are the physical distances (Mb) of the QTL, and the right side is the QTL.
Table 3 Five repetitively detected stable QTL
Fig. 4 Analysis of the LP-related QTL qLP-Gh5.18 on chromosome A05 A: Manhattan plot of association mapping of LP based on BLUP value in GLM (Q) model. Chromosomes 1 to 13 represent chromosomes A01 to A13, and 14 to 26 represent chromosomes D01 to D13. B: Localized Manhattan plot around the peak region on chromosome A05, with red arrows indicating snp497745. C: Boxplot of LP based on the snp497745 genotype. Significance analysis was performed; **** represent significance at the 0.000 1 probability level. D: LD heat map of SNP in the 108.85-109.11 Mb interval.
Table 4 Candidate genes and gene annotation for LP and BW
Fig. 5 Analysis of the LP-related QTL qLP-Gh12.43 on chromosome A12 A: Manhattan plot of association mapping of LP based on E5 in GLM (P) model. B: Localized Manhattan plot around the peak region on chromosome A12, with red arrows indicating snp1691332 in qLP-Gh12.43. C: Boxplot of LP based on the snp1691332 genotype; **** represent significance at the 0.000 1 probability level. D: LD heat map of SNP in the 106.57-106.82 Mb interval.
Fig. 6 Analysis of the LP-related QTL qLP-Gh17.2 on chromosome D04 A: Manhattan plot of association mapping of LP based on BLUP value in GLM (Q) model; B: Localized Manhattan plot around the peak region on chromosome D04, with red arrows indicating snp2180718 in qLP-Gh12.43; C: Boxplot of LP based on the snp2180718 genotype; **, ***, and **** represent significant difference at the 0.01, 0.001, and 0.000 1 probability levels, respectively. D: LD heat map of SNP in the 3.80-3.96 Mb interval.
Fig. 7 Analysis of the BW-related QTL qBW-Gh7.5 on chromosome A07 A: Manhattan plot of association mapping of BW based on BLUP value in GLM （P） model. B: Localized Manhattan plot around the peak region on chromosome A07, with red arrows indicating snp852852 in qBW-Gh7.5. C: Boxplot of BW based on the snp852852 genotype; ** represents significant difference at the 0.01 probability level. D: LD heat map of SNP in the 90.83 - 91.18 Mb interval.
Table 5 Co-localized LP-related and BW-related QTL
Fig. 8 Analysis of the BW-related QTL qBW-Gh19.5 on chromosome D06 A: Manhattan plot of association mapping of BW in E5 and GLM (Q) model. B: Localized Manhattan plot around the peak region on chromosome D06, with red arrows indicating snp2428027 in qBW-Gh19.5. C: Boxplot of BW based on the snp24280272 genotype; * represents significant difference at the 0.01 probability level. D: LD heat map of SNP in the 64.22 - 64.56 Mb interval.

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