Arabica coffee - IAC/EMBRAPA - BRAZIL

Published: 22 March 2020| Version 2 | DOI: 10.17632/whtnz2w7t9.2
Contributors:
Humberto Fanelli Carvalho,
Juliana Vieira Almeida Nonato,
Lilian Padilha,
Mirian Perez Maluf,
Oliveiro Guerreiro Filho

Description

The plant material used in this study consisted of 597 arabica coffee (Coffea arabica) plants originated from nine different progenies of self-pollination and open pollination populations, with a single check (Catuaí). The population was designed in a randomized complete block (RCBD) with nine replications installed at the Agronomic Institute of Campinas, at the experimental center “Santa Elisa”, (22°51’S, 47°04’W, 640 m). Field evaluations were carried out in 2005, 2006, 2007, and 2008 seasons for grain yield, measured in grams of fresh beans recently harvested from individual coffee plant. The resistance evaluations for coffee leaf miner (Leucoptera coffeella) and leaf rust (Hemileia vastatrix) were carried out in 2013 and 2014. Two different year period were considering, April/May (LM1) and September/October (LM2), to coffee leaf miner evaluations. The evaluation was performed as reaction type (LRrt) and lesion density (LRld) for coffee leaf rust. The DNA was extracted by following the CTAB protocol. Genomic libraries were prepared, and DNA samples were digested using the Pst1 restriction enzyme. Genotyping-by-sequencing (GBS) was carried out using an Illumina-HiSeq 2500, the reads were aligned against a reference genome of Coffea arabica (assembly Cara_1.0) (https://www.ncbi.nlm.nih.gov/genome/?term=txid13443[orgn]). The SNP calling was performed using the FreeBayes software. Missing data was imputed using the BEAGLE 5.0 software. The SNP set was filtered using VCFtools and the following parameters: (i) maintaining only biallelic markers, (ii) removing sites with a minor allelic frequency (MAF) lower than 5%; (iii) keeping markers with call rate of 80%; and (iv) markers were submitted to linkage disequilibrium (LD) pruning with r^2 > 0.99 were removed. At the end, a SNP matrix containing 4,666 SNPs was considered in the genotyping data set. The study was sponsored by Agronomic Institute of Campinas – IAC, Brazilian Agricultural Research Corporation – EMBRAPA, Secretariat of Agriculture and Supply of São Paulo State – SAASP, as part of the research fellowship CNPq DT 308.634/2016-0 and Brazilian Consortium for Coffee Research and Development projects 02.13.02.023.00.02 and 02.13.02.034.00.02. The principal investigator Dr. Oliveiro Guerreiro-Filho (oliveiro@iac.sp.gov.br) and Dr. Mirian Perez Maluf (mirian.maluf@embrapa.br), as the project designers and responsible for the data set, are correspondent authors.

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Institutions

Instituto Agronomico, Empresa Brasileira de Pesquisa Agropecuaria

Categories

Genomics, Crop Breeding, Biometrics in Plant Breeding, Statistical Prediction

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