bioRxiv Science⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.1101/2021.11.22.469505

Genome-wide association studies and genomic selection assays made in a large sample of cacao (Theobroma cacao L.) germplasm reveal significant marker-trait associations and good predictive value for improving yield potential

Bekele, F. L.·Lanaud, C.·Bidaisee, G. G.·Allegre, M.·Argout, X.·Fouet, O.·Boccara, M.·Saravanakumar, D.·Bekele, I.
View original source ↗Export metadata ↓

Abstract

A genome-wide association study was undertaken to unravel marker-trait associations (MTAs) between SNP markers and yield-related traits. It involved a subset of 421 cacao accessions from the large and diverse collection conserved ex situ at the International Cocoa Genebank Trinidad. An average linkage disequilibrium (r2) of 0.10 at 5.2 Mb was found across several chromosomes. Seventeen significant (P [≤] 8.17 x 10-5 (-log10 (p) = 4.088)) MTAs of interest, which accounted for 5 to 17% of the explained phenotypic variation, were identified using a Mixed Linear Model in TASSEL version 5.2.50. The most significant MTAs identified were related to seed number and seed length on chromosome 7 and seed number on chromosome 1. Other significant MTAs involved seed length to width ratio on chromosomes 3 and 5 and seed length on chromosomes 4 and 9. It was noteworthy that several yield-related traits, viz., seed length, seed length to width ratio and seed number were associated with markers on different chromosomes, indicating their polygenic nature. Approximately 40 candidate genes that encode embryo and seed development, protein synthesis, carbohydrate transport and lipid biosynthesis and transport were identified in this study. A significant association of fruit surface anthocyanin intensity co-localised with MYB-related protein 308 on chromosome 4. Testing of a genomic selection approach revealed good predictive value (GEBV) for economic traits such as seed number (GEBV = 0.611), seed length (0.6199), seed width (0.5435), seed length to width ratio (0.5503), seed/cotyledon mass (0.6014) and ovule number (0.6325). The findings of this study could facilitate genomic selection and marker-assisted breeding of cacao thereby expediting improvement in the yield potential of cacao planting material.

Explore related subjects

genomicsPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Bekele, F. L., Lanaud, C., Bidaisee, G. G., Allegre, M., Argout, X., Fouet, O., Boccara, M., Saravanakumar, D., Bekele, I.. 2021-11-22. Genome-wide association studies and genomic selection assays made in a large sample of cacao (Theobroma cacao L.) germplasm reveal significant marker-trait associations and good predictive value for improving yield potential. https://doi.org/10.1101/2021.11.22.469505

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Genome-wide diversity across 130 years reveals drastic post-bottleneck genetic erosion in a recovering population of golden eagles (Aquila chrysaetos)

Many wild populations have experienced severe human-induced declines, but the genetic consequences of such bottlenecks are often poorly understood. In Finland, as well as in many other countries, golden eagles were heavily persecuted during the 19th-20th centuries, disappearing from southern regions and reaching their lowest population size in the 1950-1960s. Although conservation efforts facilitated demographic recovery, the long-term genomic consequences of the bottleneck remained unknown. Here, we used whole-genome sequencing data spanning 136 years to evaluate patterns of genetic diversity in 26 Finnish golden eagles before, during, and after the mid-20th century bottleneck. We found substantial loss of genetic variation, including an 82% reduction in genome-wide heterozygosity, a 42% decline in nucleotide diversity, a 67% reduction in Watterson's theta, and a substantial loss of variable sites. Analyses of the site frequency spectrum and Tajima's D confirmed historical population contraction, and runs of homozygosity analysis indicated elevated post-bottleneck inbreeding. These results indicate strong genetic erosion in Finnish golden eagles despite the census size recovery. Therefore, incorporating genomic indicators in conservation monitoring and performing regional assessments are necessary to guide management and preserve biodiversity in line with the Global Biodiversity Framework's goal of maintaining genetic variation.

genomics↗
bioRxiv2026

Long-read analysis of complete human 5S rDNA arrays reveals a zoned organization with two-state unit methylation linked to chromatin architecture

Despite the fundamental importance of the 5S ribosomal DNA (rDNA) to all cellular life, the landscape of its units by position along its array has remained poorly understood. Here, recent telomere-to-telomere long-read sequencing is used to resolve 5S rDNA arrays from flank to flank and to follow the state of each unit along single molecules. The array is zoned at both the sequence and the epigenetic level. Notably, methylation is bimodal at the level of the unit, and the combination of low-methylation and high-methylation units gives rise to the overall methylation pattern of the array. Moreover, the average number of low-methylation units remains relatively constant regardless of array length. Chromatin fiber sequencing (Fiber-seq) data further show that low-methylation units are more accessible, have lower nucleosome occupancy and are more frequently footprinted at the TFIIIB-binding site, consistent with analyses of ATAC-seq and ChIP-seq data from cell lines. Across species, this pattern is shared among apes, whereas other species show diverse patterns. These results provide a unit-resolved view of the human 5S rDNA array and reveal a zone-specific organization of unit methylation that is associated with chromatin architecture.

genomics↗
bioRxiv2026

Using Oyster Genomics to Understand Human Health

As sessile filter feeders that experience continuous environmental exposure, oysters, particularly Crassostrea virginica, offer a unique opportunity to understand how environmental exposure alters the genome and influence health. Furthermore, oysters must be sorted by size for market value for premium size and taste. However, it requires intensive labor, specialized equipment (tumblers), and is susceptible to environmental risks like pollution. Therefore, it is desirable to produce uniform oysters without machines. However, limitations in the previous reference genome [2] have constrained our understanding of how genes are organized and maintained in oyster populations. To this end, we harvested 240 adult oysters in same location, 120 extremely large size and 120 extremely small, controlled with all confounding factors such as age and water temperature. We perform a genome wise associate study (GWAS) using next generation whole genome sequencing, aiming to discover genomic regions associated with oyster size. Using PacBio HiFi, Illumina, and Hi-C technologies, we generated a 99.7% complete chromosome-level genome assembly for C. virginica (NCBI RefSeq GCF_053477285.1) [75]. We identified a ~13 Mb region on chromosome 1 uniquely expanded in C. virginica and enriched for innate immune and stress-response genes. To evaluate whether these structural features are reflected at the population level, we then conducted a k-mer analysis. This revealed differential sequence patterns by size, including enrichment of bacterial DNA in smaller individuals and host variation at the RNF213 locus within this region. By highlighting genome structure as a mediator of immune resilience, this work supports the use of oysters as sentinels to advance out understanding of how the dynamic reassembly of the genome due to environmental exposures influence health in human populations.

genomics↗