Genetic classification of Vietnamese cacao cultivars assessed by SNP and SSR markers

Everaert, Helena; Wever, Jocelyn De; Tang, Thi Kim Hong; Vu, Thi Lam An; Maebe, Kevin; Rottiers, Hayley; Lefever, Steve; Smagghe, Guy; Dewettinck, Koen; Messens, Kathy

doi:10.1007/s11295-020-01439-x

Cited by 15 publications

(15 citation statements)

References 40 publications

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“…As cocoa genotype evolution, together with hybridization practices and breeding programs, results in special population dynamics, 43,46 molecular methods have been developed in the recognition of the resulting genetic diversity in cocoa producing‐regions. In particular, molecular marker‐based protocols and the use of single nucleotide polymorphism have been well developed for cocoa genotyping 36,53,97–99 . This methodology has been effective in the determination of provenance and geographical delimitation.…”

Section: Authentication and Geographical Differentiation Of Qualitymentioning

confidence: 99%

Quality differentiation of cocoa beans: implications for geographical indications

Hernandez

Granados²

2021

J Sci Food Agric

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Geographical indications may stimulate collective actions of governance for quality control, trade and marketing as well as innovation based on the use of local resources and regional biodiversity. Cocoa production, however, dominated by small family agriculture in tropical regions, has rarely made use of such strategies. This review is aimed at understanding major research interests and emerging technologies helpful for the origin differentiation of cocoa quality. Results from literature search and cited references of publications on cocoa research were imported into VOSviewer for data analysis, which aided in visualizing major research hotpots. Co‐occurrence analysis yielded major research clusters which guided the discussion of this review. Observed was a consensus recognizing cocoa quality resulting from the interaction of genotype, fermentation variables and geographical origin. A classic view of cocoa genetics based on the dichotomy of ‘fine versus bulk’ has been reexamined by a broader perspective of human selection and cocoa genotype evolution. This new approach to cocoa genetic diversity, together with the understanding of complex microbiome interactions through fermentation, as well as quality reproducibility challenged by geographical conditions, have demonstrated the importance of terroir in the production of special attributes. Cocoa growing communities around the tropics have been clearly enabled by new omics and chemometrics to systematize producing conditions and practices in the designation of specifications for the differentiation of origin quality. © 2021 Society of Chemical Industry

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Section: Authentication and Geographical Differentiation Of Qualitymentioning

confidence: 99%

Quality differentiation of cocoa beans: implications for geographical indications

Hernandez

Granados²

2021

J Sci Food Agric

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“…Two cacao genomes have been sequenced and assembled [22,23], thousands of SNPs were discovered and gathered in user-friendly, high-precision genotyping platforms [24][25][26], and a large number of germplasm accessions genotyped. Despite the many applications of SNPs in cacao genetics and breeding, including diversity studies [27][28][29][30], QTL mapping, genome-wide association and genomic selection [31][32][33][34][35][36], they have not been used to accelerate the development of inbred lines. Nevertheless, population and individual level estimated heterozygosity have been published for cacao germplasm collections and wild populations using microsatellites [37][38][39][40] or hundreds of SNPs [41,42].…”

Section: Introductionmentioning

confidence: 99%

Genome-wide SNP genotyping as a simple and practical tool to accelerate the development of inbred lines in outbred tree species: an example in cacao (Theobroma cacao L.)

Lopes

Pires

Gramacho

et al. 2022

Preprint

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Cacao is a globally important crop with a long history of domestication and selective breeding. Despite the increased use of elite clones by cacao farmers, worldwide plantations are established mainly using hybrid progeny material derived from heterozygous parents, therefore displaying high tree-to-tree variability. The deliberate development of hybrids from advanced inbred lines produced by successive generations of self-pollination has not yet been fully considered in cacao breeding. This is largely due to the self-incompatibility of the species, the long generation cycles (3-5 years) and the extensive trial areas needed to accomplish the endeavor. We propose a simple and accessible approach to develop inbred lines based on accelerating the buildup of homozygosity based on regular selfing assisted by genome-wide SNP genotyping. In this study we genotyped 90 clones from the Brazilian CEPEC's germplasm collection and 49 inbred offspring of six S 1 or S 2 cacao families derived from self-pollinating clones CCN-51, PS-13.19, TSH-1188 and SIAL-169. A set of 3,380 SNPs distributed across the cacao genome were interrogated on the EMBRAPA multi-species 65k Infinium chip. The 90 cacao clones showed considerable variation in genome-wide SNP homozygosity (mean 0.727 ± 0.182) and 19 of them with homozygosity >90%. By assessing the increase in homozygosity across two generations of self-pollinations, SNP data revealed the wide variability in homozygosity within and between S 1 and S 2 families. Even in small families (<10 sibs), individuals were identified with up to ~1.5 standard deviations above the family mean homozygosity. From baseline homozygosities of 0.476 and 0.454, offspring with homozygosities of 0.862 and 0.879 were recovered for clones TSH-1188 and CCN-51 respectively, in only two generations of selfing (81-93% increase). SNP marker assisted monitoring and selection of inbred individuals can be a practical tool to optimize and accelerate the development of inbred lines of outbred species. This approach will allow a faster and more accurate exploitation of hybrid strategies in cacao breeding programs and potentially in other perennial fruit and forest trees.

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“…Population genetics of plants have long been assessed using molecular markers, including simple sequence repeat (SSR), amplified fragment length polymorphism (AFLP), random amplified polymorphic DNA (RAPD), and expressed sequence tag SSR ( Yilmaz, 2016 ; Stone et al., 2019 ; Everaert et al., 2020 ; Wagutu et al., 2020 ). Recently, single nucleotide polymorphism (SNPs) based on next-generation sequencing (NGS) have become the markers of choice for determining population structure because they are abundant, stable in the genome, and can be accurately scored ( Deschamps et al., 2012 ).…”

Section: Introductionmentioning

confidence: 99%

Genetic diversity and structure of Rhododendron meddianum, a plant species with extremely small populations

Zhang

Liu

et al. 2021

Plant Diversity

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Rhododendron meddianum is a critically endangered species with important ornamental value and is also a plant species with extremely small populations. In this study, we used double digest restriction-site-associated DNA sequencing (ddRAD) technology to assess the genetic diversity, genetic structure and demographic history of the three extant populations of R. meddianum . Analysis of SNPs indicated that R. meddianum populations have a high genetic diversity (π = 0.0772 ± 0.0024, H E = 0.0742 ± 0.002). Both F ST values (0.1582–0.2388) and AMOVA showed a moderate genetic differentiation among the R. meddianum populations. Meanwhile, STRUCTURE, PCoA and NJ trees indicated that the R. meddianum samples were clustered into three distinct genetic groups. Using the stairway plot, we found that R. meddianum underwent a population bottleneck about 70,000 years ago. Furthermore, demographic models of R. meddianum and its relative, Rhododendron cyanocarpum , revealed that these species diverged about 3.05 (2.21–5.03) million years ago. This divergence may have been caused by environmental changes that occurred after the late Pliocene, e.g., the Asian winter monsoon intensified, leading to a drier climate. Based on these findings, we recommend that R. meddianum be conserved through in situ , ex situ approaches and that its seeds be collected for germplasm.

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Genetic classification of Vietnamese cacao cultivars assessed by SNP and SSR markers

Cited by 15 publications

References 40 publications

Quality differentiation of cocoa beans: implications for geographical indications

Quality differentiation of cocoa beans: implications for geographical indications

Genome-wide SNP genotyping as a simple and practical tool to accelerate the development of inbred lines in outbred tree species: an example in cacao (Theobroma cacao L.)

Genetic diversity and structure of Rhododendron meddianum, a plant species with extremely small populations

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