A new set of quantitative trait loci linked to lipid content in <i>Coffea arabica</i>

Muniz, Herison Victor Lima; Ariyoshi, Caroline; Ferreira, Rafaelle Vecchia; Felicio, Mariane Silva; Pereira, Luiz Filipe Protasio

doi:10.1590/1984-70332024v24n2a25

Herison Victor Lima Muniz

Universidade Tecnológica Federal do Paraná, Avenida Alberto Carazzai, 1640, Centro, 86300-000, Cornélio Procópio, PR, Brazil

Instituto de Desenvolvimento Rural do Paraná, Rodovia Celso Garcia Cid, km 375, Vivendas do Arvoredo, 86047-902, Londrina, PR, Brazil.

Caroline Ariyoshi

Instituto de Desenvolvimento Rural do Paraná, Rodovia Celso Garcia Cid, km 375, Vivendas do Arvoredo, 86047-902, Londrina, PR, Brazil.

Rafaelle Vecchia Ferreira

Instituto de Desenvolvimento Rural do Paraná, Rodovia Celso Garcia Cid, km 375, Vivendas do Arvoredo, 86047-902, Londrina, PR, Brazil.

Mariane Silva Felicio

Universidade Estadual Paulista “Júlio de Mesquita Filho”, Rua Professor Doutor Antônio Celso Wagner Zanin, 250, Distrito de Rubião Junior, 18618-689, Botucatu, SP, Brazil

Luiz Filipe Protasio Pereira

Instituto de Desenvolvimento Rural do Paraná, Rodovia Celso Garcia Cid, km 375, Vivendas do Arvoredo, 86047-902, Londrina, PR, Brazil.

Embrapa Café, Parque Estação Biológica, PQEB W3, 70770-901, Brasília, DF, Brazil

https://orcid.org/0000-0002-4872-6607

* E-mail: filipe.pereira@embrapa.br

Figures (3)
Tables (3)

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Figure 1
Manhattan plots (A-B) of the single-locus genome-wide association study for lipid content using the GLM and MLM methods. The x-axis represents the chromosomes, and the y-axis represents the −log₁₀(p-value). The solid line indicates the thresholds for lipid content in C. arabica. Quantile-quantile (Q-Q) plots (C-D) of a single-locus genome-wide association study for lipid content in C. arabica. Q-Q plots show the observed vs. expected negative log₁₀ p-values.

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Figure 2
Manhattan plots (A-E) of the multi-locus genome-wide association study for lipid content with the methods mrMLM, FASTmrMLM, FASTmrEMMA, ISIS EM-BLASSO, and FarmCPU with the PCA + K models. The x-axis represents the chromosomes, and the y-axis represents the −log₁₀(p-value). The dashed lines indicate the LOD score threshold and the solid line indicates the −log₁₀(p-value) threshold for lipid content in C. arabica. Quantile-quantile (Q-Q) plots (F-J) of a multi-locus genome-wide association study for lipid content in C. arabica with the PCA + K models. Q-Q plots show the observed vs. expected negative log₁₀ p-values.

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Figure 3
Manhattan plots (A-D) of the multi-locus genome-wide association study for lipid content with the methods mrMLM, FASTmrMLM, ISIS EM-BLASSO, and FarmCPU with the Q + K models. The x-axis represents the chromosomes, and the y-axis represents the −log₁₀(p-value). The dashed lines indicate the LOD score threshold, and the solid line indicates the −log₁₀(p-value) threshold, for lipid content in C. arabica. Quantile-quantile (Q-Q) plots (E-H) of a multi-locus genome-wide association study for lipid content in C. arabica with the Q + K models. Q-Q plots show the observed vs. expected negative log₁₀ p-values.

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Table 1
Associated QTNs in the multi-locus mrMLM, FASTmrMLM, FASTmrEMMA ISIS-EM-BLASSO, and FarmCPU methods adjusted by PCA + K models

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Table 2
Associated QTNs in the multi-locus mrMLM, FASTmrMLM, ISIS-EM-BLASSO, and FarmCPU methods adjusted by Q + K models

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Table 3
Functional annotation of genes close to QTNs associated with lipids in Coffea arabica

		mrMLM		FASTmrMLM		FASTmrEMMA		ISIS EM-BLASSO		FarmCPU
Position of QTN in the genome of C. arabica Et039*	Allele change	−log10 (p-value)	LOD SCORE	−log10 (p-value)	LOD SCORE	−log10 (p-value)	LOD SCORE	−log10 (p-value)	LOD SCORE	−log10 (p-value)
Chr_0_4635_168274	T/C			5.6818	4.8901			4.8566	4.1001	3.488117
Chr_1_sg_C_22364613	T/C	4.8608	4.1041
Chr_1_sg_C_31802172	T/C	5.3237	4.5466
Chr_2_sg_C_56859771	A/G	5.3267	4.5495							3.335358
Chr_7_sg_C_11717962	A/G	4.7552	4.0035
Chr_7_sg_C_409622	G/A	4.4578	3.7205
Chr_8_sg_C_19869722	A/G			4.9522	4.1914			5.4941	4.71	3.326979
Chr_2_sg_E_ 58841892	A/G									3.411168
Chr_2_sg_E_ 60056603	A/G									4.082494
Chr_5_sg_E_35714509	T/C	6.1815	5.3709
Chr_7_sg_E_20849219	T/C			4.1472	3.4261	3.9487	3.2386
Chr_8_sg_E_34967946	T/C	6.5827	5.758
Chr_11_sg_E_29236376	A/G	6.0433	5.2378

		mrMLM		FASTmrMLM		ISIS EM-BLASSO		FarmCPU
Position of QTN in the genome of C. arabica Et039*	Allele change	−log10 (p-value)	LOD SCORE	−log10 (p-value)	LOD SCORE	−log10 (p-value)	LOD SCORE	−log10 (p-value)
Chr_0_4635_168274	T/C	4.2953	3.5664	4.8379	4.0823	7.2502	6.4039
Chr_6_sg_C_4567047	C/T							3.286509
Chr_8_sg_C_19869722	A/G	4.4391	3.7028	3.6986	3.0031			3.338187
Chr_2_sg_E_60056603	A/G	4.3333	3.6024					3.546682
Chr_7_sg_E_20849219	T/C	5.3459	4.5679	4.353	3.6211	4.0384	3.3233
Chr_11_sg_E_29236360	A/G			3.8991	3.1918	4.6147	3.8697

Gene¹	QTN	Gene position in relation to the QTN²	Functional annotation³
g15.102	Chr_6_sg_C_4567047	(+) 27.242	4 -phosphopantetheinyl transferase isoform X1
g1.69	Chr_7_sg_C_409622	(-) 172.382	senescence-associated carboxylesterase 101-like isoform X1
g10.11	Chr_7_sg_C_409622	(+) 46.483	patatin 3
g10.29	Chr_7_sg_C_409622	(+) 87.019	triacylglycerol lipase-like 1
g10.8	Chr_7_sg_C_409622	(+) 138.414	patatin 1
g66.10	Chr_8_sg_C_19869722	(+) 46.073	3-ketoacyl- synthase 10
g119.153	Chr_5_sg_E_35714509	(+) 19.826	electron transfer flavo subunit mitochondrial

[1] * E-mail: filipe.pereira@embrapa.br

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A new set of quantitative trait loci linked to lipid content in Coffea arabica

Abstract