Inbreeding depression in cocoa (Theobroma cacao L) over generations

NARAYANAPUR, VIJAYAKUMAR B; Suma, B.; Minimol, J. S.; Santoshkumar, A V; Mathew, Deepu

doi:10.21203/rs.3.rs-1294912/v1

Cited by 2 publications

(1 citation statement)

References 6 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Reports on estimates of inbreeding depression following self-fertilization in cacao are scarce and limited to a few clones. The few reports have shown little if any inbreeding depression for a number of traits and occasionally even positive effects of inbreeding [ 65 , 74 , 75 ]. These observations, albeit requiring further validation, are in line with the fact that many currently planted clones already show moderate to high levels of inbreeding such as the Amelonado selection SIAL-169 ( S4 File ), resulting from differential inbreeding life histories.…”

Section: Discussionmentioning

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

Pires²,

Gramacho³

et al. 2022

PLoS ONE

View full text Add to dashboard Cite

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 S1 or S2 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 S1 and S2 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 tree species. This approach will allow a faster and more accurate exploitation of hybrid breeding strategies in cacao improvement programs and potentially in other perennial fruit and forest trees.

show abstract

Section: Discussionmentioning

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

Pires²,

Gramacho³

et al. 2022

PLoS ONE

View full text Add to dashboard Cite

show abstract

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

View full text Add to dashboard Cite

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.

show abstract

Inbreeding depression in cocoa (Theobroma cacao L) over generations

Cited by 2 publications

References 6 publications

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.)

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.)

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.)

Contact Info

Product

Resources

About