SNP markers associated with resistance to frosty pod and black pod rot diseases in an F1 population of Theobroma cacao L.

Osman A Gutiérrez,Guiliana Mustiga,Donald Livingstone,Stefan Royaert,Bryan A Bailey,Juan Carlos Motamayor,Wilbert Phillips-Mora,Keithanne Mockaitis,Raymond J Schnell,Alina S Puig,Shahin S Ali

doi:10.1007/s11295-021-01507-w

Abstract

Economically, cacao (Theobroma cacao L.) is a major tropical commodity for the Americas; however, severe losses due to Moniliophthora roreri (Cif. and Par.), which causes frosty pod rot (FPR), and Phytophthora spp., which causes black pod rot (BPR), have reduced cacao production in the Americas. The objectives of this study are to (i) re-confirm the QTL using different marker set; (ii) discover new QTL associated with FPR and BPR resistance using SNP markers; and (iii) find genes in the candidate QTL regions. At CATIE in Turrialba, Costa Rica, an F1 mapping population of cacao was obtained by crossing “POUND 7,” a clone moderately susceptible to FPR and resistant to BPR, with “UF 273,” resistant to FPR and highly susceptible to BPR. A total of 179 F1 progeny were fingerprinted with 5149 SNP markers and a dense linkage map composed of 10 linkage groups was developed using 2910 polymorphic SNP markers. Also segregating F1 trees were screened for resistance to FPR and BPR diseases. Seven QTL previously reported on chromosomes 2, 7, and 8 for FPR resistance and on chromosomes 4, 8, and 10 for BPR resistance were confirmed. Additionally, eight QTL were identified for FPR resistance (chromosomes 4, 9, and 10) and BPR resistance (chromosome 2). The expression of genes commonly associated with plant defense and disease resistance that are located within the identified QTL was confirmed.

Highlights

IntroductionCacao (Theobroma cacao L.) is an evergreen tree indigenous to the Amazon basin
A heterozygous F1 mapping population was developed at Centro Agronómico Tropical de Investigación y Enseñanza (CATIE) by crossing “POUND 7,” a clone moderately susceptible to frosty pod rot (FPR) and resistant to black pod rot (BPR), with “UF 273,” which is resistant to FPR and highly susceptible to BPR (Phillips-Mora et al 2013)
A consensus linkage map was built from an F1 population of 179 individuals from a cross between “UF 273” Type I and “POUND 7” containing 1883 unique loci and spanning 1036.72 cM, with an average marker interval of 0.93 cM

Summary

Introduction

Cacao (Theobroma cacao L.) is an evergreen tree indigenous to the Amazon basin. It can be found growing in many countries between latitudes 20° S and 20° N (Cope 1984). It was thought that cacao was domesticated in Mesoamerica by the Olmec, who transferred their knowledge to the Toltec, Mayan, and Aztec civilizations (Bartley 2005; Coe and Coe 2013). Recent findings by Zarrillo et al (2018) indicated that the cacao center of diversity was located on the upper Amazon region of northwest South America, which was the center of domestication. Theobroma cacao is a diploid species (2n = 2x = 20) within the family Malvaceae (Whitlock and Baum 1999), initially divided into three major morphological/geographic groups: Criollo, Forastero, and

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