Summary
Coffee species such as
Coffea canephora
P. (Robusta) and
C. arabica
L. (Arabica) are important cash crops in tropical regions around the world.
C. arabica
is an allotetraploid (2
n
= 4
x
= 44) originating from a hybridization event of the two diploid species
C. canephora
and
C. eugenioides
(2
n
= 2
x
= 22). Interestingly, these progenitor species harbour a greater level of genetic variability and are an important source of genes to broaden the narrow Arabica genetic base. Here, we describe the development, evaluation and use of a single‐nucleotide polymorphism (
SNP
) array for coffee trees. A total of 8580 unique and informative
SNP
s were selected from
C. canephora
and
C. arabica
sequencing data, with 40% of the
SNP
located in annotated genes. In particular, this array contains 227 markers associated to 149 genes and traits of agronomic importance. Among these, 7065
SNP
s (~82.3%) were scorable and evenly distributed over the genome with a mean distance of 54.4 Kb between markers. With this array, we improved the Robusta high‐density genetic map by adding 1307
SNP
markers, whereas 945
SNP
s were found segregating in the Arabica mapping progeny. A panel of
C. canephora
accessions was successfully discriminated and over 70% of the
SNP
markers were transferable across the three species. Furthermore, the canephora‐derived subgenome of
C. arabica
was shown to be more closely related to
C. canephora
accessions from northern Uganda than to other current populations. These validated
SNP
markers and high‐density genetic maps will be useful to molecular genetics and for innovative approaches in coffee breeding.
Key message
High variability for and candidate loci associated with resistance to southern anthracnose and clover rot in a worldwide collection of red clover provide a first basis for genomics-assisted breeding.
Abstract
Red clover (Trifolium pratense L.) is an important forage legume of temperate regions, particularly valued for its high yield potential and its high forage quality. Despite substantial breeding progress during the last decades, continuous improvement of cultivars is crucial to ensure yield stability in view of newly emerging diseases or changing climatic conditions. The high amount of genetic diversity present in red clover ecotypes, landraces, and cultivars provides an invaluable, but often unexploited resource for the improvement of key traits such as yield, quality, and resistance to biotic and abiotic stresses. A collection of 397 red clover accessions was genotyped using a pooled genotyping-by-sequencing approach with 200 plants per accession. Resistance to the two most pertinent diseases in red clover production, southern anthracnose caused by Colletotrichum trifolii, and clover rot caused by Sclerotinia trifoliorum, was assessed using spray inoculation. The mean survival rate for southern anthracnose was 22.9% and the mean resistance index for clover rot was 34.0%. Genome-wide association analysis revealed several loci significantly associated with resistance to southern anthracnose and clover rot. Most of these loci are in coding regions. One quantitative trait locus (QTL) on chromosome 1 explained 16.8% of the variation in resistance to southern anthracnose. For clover rot resistance we found eight QTL, explaining together 80.2% of the total phenotypic variation. The SNPs associated with these QTL provide a promising resource for marker-assisted selection in existing breeding programs, facilitating the development of novel cultivars with increased resistance against two devastating fungal diseases of red clover.
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