Biology subjects

Ceballos, H.

Publications and source records attributed to Ceballos, H..

2 recordsLinked to original sources

bioRxiv2023

Pan-genome and Haplotype Map of Cultivars and Their Wild Ancestors Provides Insights into Adaptive Evolution of Cassava (Manihot esculenta Crantz)

Cassava is the most important starch sources, a tropical model crop. We constructed nearly T2T genomes of cultivar AM560, wild ancestors FLA4047 and W14, pan-genome of 24 representatives and a clarified evolutionary tree with 486 accessions. Comparison of SVs and SNVs between the ancestors and cultivated cassavas revealed predominant expansion, contraction of genes and gene families. Significantly selective sweeping occurred in the cassava genomes in 122 footprints with 1,519 candidate domestication genes. We identified selective mutations in MeCSK and MeFNR3 promoting photoreaction associated with MeNADP-ME of C4 assimilation in modern cassava. Co-evolved retardation of floral primordia and initiation of storage roots arose from MeCOL5 mutants with altered bindings to MeFT1, MeFT2 and MeTFL2. MebHLHs evolved to regulate the biosynthesis, transport and endogenous remobilization of cyanogenic glucosides, with new functionalities of MeMATE1, MeGTR in selected sweet cassava. These findings enhanced comprehensive knowledge and database on the evolution and breeding of cassava. HIGHLIGHTSO_LIThree nearly T2T cassava genomes of cultivar AM560 and its wild ancestors FLA4047 and W14. C_LIO_LIA species-level cassava panSV haplotype map across 346,322 structural variations over 31,362 gene families and 96,032,008 SNPs and InDels variations globally and a clarified evolutionary tree with 486 accessions. C_LIO_LISelective mutations in MeCSK and MeFNR3 promoted photoreaction associated with MeNADP-ME of C4 assimilation shaped the C3-C4 intermediate photosynthesis of modern cassava. C_LIO_LICoevolution of floral primordia contrary to initiated storage root is pivotal for the domestication of cassava, and arose from MeCOL5 mutants altered the binding with MeFT1, MeFT2 (SP6A), and MeTFL2. C_LI

systems biology↗

bioRxiv2022

Validation of SNP markers for marker-assisted selection of genotypes with increased carotenoid and dry matter contents in cassava

Provitamin A biofortification and increased dry matter content are important breeding targets in cassava improvement programs worldwide. Biofortified varieties contribute to the alleviation of provitamin A deficiency, a leading cause of preventable blindness in developing countries. Dry matter content is a major component of dry yield and thus underlies overall variety performance and acceptability by growers, processors, and consumers. SNP markers linked to these traits have recently been discovered through several genome-wide association studies but have not been deployed for marker-assisted selection (MAS). Assessment of marker performance in diverse genetic backgrounds is an important step towards their deployment for routine MAS. In the present study, seven previously identified markers for these traits were converted to a robust set of uniplex allele-specific PCR assays and validated in two independent pre-breeding and breeding populations. These assays were efficient in discriminating marker genotypic classes and had an average call rate greater than 98%. A high correlation was observed between the predicted and observed carotenoid content as inferred by root yellowness intensity in the breeding (r = 0.92) and pre-breeding (r = 0.95) populations. On the other hand, dry matter content-markers had moderately low predictive accuracy in both populations (r < 0.40) due to the more quantitative nature of the trait. This work confirmed marker effectiveness in multiple backgrounds, therefore, further strengthening its value in cassava biofortification to ensure nutritional security as well as dry matter content productivity. Our study provides a framework to guide future marker development, thus leading to more routine use of markers in MAS in cassava improvement programs.

genomics↗