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	基因ID Gene ID	染色体 Chromosome	位置 Position/bp	拟南芥中同源基因 Homologous gene in Arabidopsis	功能注释 Functional annotation
LP	GH_A05G4223	A05	108 940 857~ 108 942 463	AT5G05340.1	编码蛋白质序列与参与木质素生物合成的过氧化物酶相似，功能突变缺失表现为木质部纤维发育异常和木质素生物合成酶活性降低 Encodes a protein with sequence similarity to peroxidases that is involved in lignin biosynthesis. Loss of function mutations show abnormal development of xylem fibers and reduced acti- vity of lignin biosynthetic enzymes
	GH_A05G4224	A05	108 950 710~ 108 951 750	AT2G40470.1	含有LOB结构域的蛋白，作为木质部细胞分化主调控因子VND7的调控因子参与木质部分化调控 LOB-domain containing protein, involved in the regulation of xylem differentiation, as a regu- lator of VND7, a master regulator of xylem cell differentiation
	GH_A05G4226	A05	108 992 628~108 995 062	AT2G40480.1	WEB家族蛋白（DUF827） WEB family protein (DUF827)
	GH_A05G4227	A05	109 051 197~109 052 912	AT3G10960.1	编码绒毛曲霉腺嘌呤-鸟嘌呤-次黄嘌呤转运体AzgA的同源物 Encodes a homolog of the adenine-guanine- hypoxanthine transporter AzgA of Aspergillus nidulans
	GH_A05G4228	A05	109 086 057~109 090 055	AT1G61670.2	Lung七跨膜受体家族蛋白 Lung seven transmembrane receptor family protein
	GH_A05G4229	A05	109 090 769~109 095 282	AT2G40700.1	DEAD-box解旋酶家族蛋白 DEAD-box helicase family protein
	GH_A05G4230	A05	109 097 260~109 099 883	AT2G40690.3	编码1种假定的二羟丙酮磷酸还原酶，参与叶绿体甘油-3-磷酸的供应 Encodes a putative dihydroxyacetone phosphate (DHAP) reductase involved in glycerol- 3-phosphate supply within the chloroplast for synthesis of glycerolipids
	GH_A12G2883	A12	106 748 735~106 749 962	AT4G02750.1	四肽重复样超家族蛋白 Tetratricopeptide repeat-like superfamily protein
	GH_A12G2884	A12	106 751 601~106 756 487	AT1G13160.1	ARM重复超家族蛋白 ARM repeat superfamily protein
	GH_A12G2885	A12	106 758 251~106 762 392	AT1G57820.3	编码包含645个氨基酸的甲基胞嘧啶结合蛋白，包含1个PHD结构域、2个环指结构域和1个SRA结构域 Encodes a 645-amino acid methylcytosine- binding protein, contains 1 PHD structural domain, 2 ring finger structural domains and 1 SRA structural domain
	GH_A12G2886	A12	106 773 820~106 774 134	AT3G18100.1	R2R3转录因子基因家族的成员 Member of the R2R3 transcription factor gene family
	GH_A12G2887	A12	106 780 464~106 783 145	AT4G02750.1	五肽重复蛋白 Pentatricopeptide repeat-containing protein
	GH_A12G2888	A12	106 785 458~106 790 726	AT3G18040.4	MAP激酶（MAPK9）相似的蛋白 Encodes a protein with similarity to MAP kinases (MAPK9)
	GH_D04G0279	D04	3 835 441~ 3 835 718	AT1G28130.1	编码IAA -氨基合成酶，在体外将天冬氨酸和其他氨基酸结合到生长素上 Encodes an IAA-amido synthase that conjugates Asp and other amino acids to auxin in vitro
	GH_D04G0280	D04	3 843 564~ 3 845 715	AT2G26790.2	五肽重复超家族蛋白 Pentatricopeptide repeat superfamily protein
	GH_D04G0281	D04	3 849 170~ 3 849 783	AT5G09810.1	肌动蛋白基因家族成员 Member of actin gene family
	GH_D04G0282	D04	3 869 577~ 3 870 189	AT2G02730.3
BW	GH_A07G2234	A07	91 011 268~ 91 011 273	AT5G48500.1	RIN4样NOI家族成员 Member of the RIN4-like NOI family
	GH_A07G2235	A07	91 058 898~ 91 059 478	AT4G12970.1	编码1个富含半胱氨酸的多肽，是1种在叶肉细胞中产生的分泌因子，作用于表皮以促进气孔的形成 Encodes a cysteine-rich peptide, a secretory factor produced in leaf pulp cells that acts on the epidermis to enhance stomatal formation
	GH_A07G2236	A07	91 061 847~ 91 062 251	AT3G07420.1	编码1个天冬酰氨酰-tRNA合成酶 Encodes an asparaginyl-tRNA synthetase
	GH_A07G2237	A07	91 065 703~ 91 066 467	AT5G48540.1	受体样蛋白激酶相关家族蛋白 Receptor-like protein kinase-related family protein
	GH_A07G2243	A07	91 182 137~ 91 183 569	AT4G13000.1	AGC（cAMP依赖性、cGMP依赖性蛋白激酶C）激酶家族蛋白 AGC (cAMP-dependent, cGMP-dependent and protein kinase C) kinase family protein
	GH_D06G2300	D06	64 362 627~ 64 366 558	AT1G29670.2	GDSL酯酶/酰基转移酶/脂肪酶 GDSL-motif esterase/acyltransferase/lipase
	GH_D06G2301	D06	64 368 830~ 64 370 862	AT1G29760.1	花粉中参与脂滴生物形成的膜蛋白 Membrane protein involved in lipid droplet biogenesis primarily in pollen
	GH_D06G2302	D06	64 371 910~ 64 372 102	AT4G18910.1	编码1个水通道蛋白同源物 Encodes an aquaporin homolog

Table 4 Candidate genes and gene annotation for LP and BW

Other figure/table from this article

Table 1 The origins of 300 cotton germplasm materials
Table 2 Statistical analysis of lint percentage and boll weight
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.
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.

模态框（Modal）标题

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