Whole-genome resequencing of Coffea arabica L. (Rubiaceae) genotypes identify SNP and unravels distinct groups showing a strong geographical pattern

Mekbib, Yeshitila; Tesfaye, Kassahun; Dong, Xiang; Saina, Josphat K.; Hu, Guang‐Wan; Wang, Qingfeng

doi:10.1186/s12870-022-03449-4

Cited by 15 publications

(13 citation statements)

References 74 publications

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“…Interestingly, we identified 98,700 (0.44%) InDels and 63,341 SNPs (0.036%) with disruptive impact on the protein ( Tables 1 , 2 and Supplementary Table 3 ). These findings are in accordance with previous similar studies on whole genome resequencing of Prunus species, Coffea arabica , and Moso bamboo ( Shirasawa et al, 2017 ; Xanthopoulou et al, 2020 ; Mekbib et al, 2022 ). Usually, the gene function is not affected by the synonymous SNPs; however, the moderate (possible non-synonymous substitution) and the high impact list of variants within Ph.…”

Section: Resultssupporting

confidence: 93%

Study of genetic variation and its association with tensile strength among bamboo species through whole genome resequencing

2022

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Moso bamboo (Phyllostachys edulis) is a versatile plant species that is widely used as a construction material by many low-income countries due to the lack of major construction materials such as steel and reinforced concrete. It is also widely used in China. Bamboo is an economically sustainable material that behaves exceptionally in natural disasters such as earthquakes and it can offer viable solutions for contemporary engineering challenges. Despite bamboo’s potential in the engineering sector, biological features such as its long generation time, its large genome size, and its polyploidy are constraining factors for genetic and genomic studies that potentially can assist the breeding efforts. This study re-sequenced 8 Phyllostachys species and 18 natural accessions of Ph. edulis, generating a large set of functionally annotated molecular markers (Single Nucleotide Polymorphisms (SNPs) and InDels) providing key genomic resource information. Moreover, all this genomic information was used to carry out a preliminary genome-wide association analysis and several candidate genes were identified to be correlated with a mechanical property that is of high interest to structural engineers: its tensile strength normal to its fibers (i.e., splitting).

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Section: Resultssupporting

confidence: 93%

Study of genetic variation and its association with tensile strength among bamboo species through whole genome resequencing

2022

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“…With the decreasing cost of sequencing and increasing large-scale and single-species sequencing projects e.g. (37)(38)(39)(40)(41)(42)(43), the number of datasets suitable for such analyses is set to rapidly increase in the near future.…”

Section: Discussionmentioning

confidence: 99%

“…The goals of our study were thus two-fold: i) to contribute to a mechanistic understanding of pest resistance in Thlaspi arvense, and, more generally, ii) to explore whether non-target reads from plant sequencing can be used as proxies for studying plant biotic interactions. Considering that we are moving towards an increasingly sequencing-prone world, where more and larger datasets are being generated for many species (37)(38)(39)(40)(41)(42)(43), the use of non-target reads will likely have very broad potential.…”

Section: Introductionmentioning

confidence: 99%

Discarded sequencing reads uncover natural variation in pest resistance inThlaspi arvense

Galanti,

Jung,

Müller

et al. 2023

Preprint

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Understanding the genomic basis of natural variation in plant pest resistance is an important goal in plant science, but it usually requires large and labour-intensive phenotyping experiments. Here, we explored the possibility that non-target reads from plant DNA sequencing can serve as phenotyping proxies for addressing such questions. We used data from a whole-genome and -epigenome sequencing study of 207 natural lines of field pennycress (Thlaspi arvense) that were grown in a common environment and spontaneously colonized by aphids, mildew and other microbes. We found that the numbers of non-target reads assigned to the pest species differed between populations, had significant SNP-based heritability, and were associated with climate of origin and baseline glucosinolate contents. Specifically, pennycress lines from cold and thermally fluctuating habitats, presumably less favorable to aphids, showed higher aphid DNA load, i.e. decreased aphid resistance. Genome-wide association analyses identified genetic variants at known defense genes but also novel genomic regions associated with variation in aphid and mildew DNA load. Moreover, we found several differentially methylated regions associated with pathogen loads, in particular differential methylation at transposons and hypomethylation in the promoter of a gene involved in stomatal closure, likely induced by pathogens. Our study provides first insights into the defense mechanisms of Thlaspi arvense, a rising crop and model species, and it demonstrates that non-target whole genome sequencing reads, usually discarded, can be leveraged to estimate intensities of plant biotic interactions. With rapidly increasing numbers of large sequencing datasets worldwide, this approach should have broad application in fundamental and applied research.

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“…Previous studies on coffee using various molecular markers reported the narrow genetic base and the low level of genetic diversity in ex-situ conserved arabica coffee germplasm accessions, cultivated varieties and elite breeding lines of arabica coffee outside of Ethiopia (Anthony et al, 2002;Maluf et al, 2005;Missio et al, 2011;Geleta et al, 2012;Al-Murish et al, 2013;Scalabrin et al, 2020). On the other hand, moderate to a high level of genetic diversity was reported among arabica coffee germplasm accessions established in ex-situ field genebank in different countries including Ethiopia (Anthony et al, 2001;Moncada and McCouch, 2004;López-Gartner et al, 2009;Mekbib et al, 2022) and specifically in forest coffee populations and farmers' cultivars in Ethiopia (Aga et al, 2005;Al-Murish et al, 2013;Tesfaye et al, 2014) using various DNA markers.…”

Section: Introductionmentioning

confidence: 99%

Assessment of Genetic Diversity among Elite Breeding Lines of Arabica Coffee (Coffea arabica L.) in Ethiopia using Simple Sequence Repeats Markers

Benti¹,

Gebre²,

Tesfaye³

et al. 2022

American Journal of Biochemistry and Biotechnology

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Despite being the center of origin and genetic diversity, there has been limited application of molecular markers in arabica coffee breeding in Ethiopia. In this study, the extent of genetic diversity and relationships of 48 elite breeding lines of arabica coffee from different geographical origins were evaluated using 14 SSR markers. The SSR markers amplified 105 alleles of which 104 are polymorphic with an average of 7.4 polymorphic alleles per locus. The average percent of polymorphism and Polymorphic Information Content (PIC) of the SSR markers were 98.81 and 0.79, respectively. The average genetic similarity coefficient among all possible pairs was 0.37 and ranged from 0.39 to 0.46 within the same geographical origin. The Unweighted Pair Group Method Using Arithmetic averages (UPGMA) cluster analysis placed the studied breeding lines into seven clusters with Jaccard's similarity coefficient of <0.44. The results of this study demonstrated the powerfulness of the SSR markers and the presence of a high level of genetic diversity and wide genetic dissimilarity within and among elite breeding lines from the same and different geographical origins. The observed diversity could be utilized in the breeding program to improve productivity and maintain the typical quality profile of origin-based landrace coffees. The SSR markers could be used in future genetic analysis of arabica coffee germplasm to increase the efficiency of the breeding program in Ethiopia. The studied breeding lines could also be conserved and managed as an important source of genetic variability to be used in the future coffee improvement program.

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Whole-genome resequencing of Coffea arabica L. (Rubiaceae) genotypes identify SNP and unravels distinct groups showing a strong geographical pattern

Cited by 15 publications

References 74 publications

Study of genetic variation and its association with tensile strength among bamboo species through whole genome resequencing

Study of genetic variation and its association with tensile strength among bamboo species through whole genome resequencing

Discarded sequencing reads uncover natural variation in pest resistance inThlaspi arvense

Assessment of Genetic Diversity among Elite Breeding Lines of Arabica Coffee (Coffea arabica L.) in Ethiopia using Simple Sequence Repeats Markers

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