Abstract
Cassava (Manihot esculenta Crantz) is a major tuberous crop produced worldwide. In this study, we sequenced 158 diverse cassava varieties and identified 349,827 single-nucleotide polymorphisms (SNPs) and indels. In each chromosome, the number of SNPs and the physical length of the respective chromosome were in agreement. Population structure analysis indicated that this panel can be divided into three subgroups. Genetic diversity analysis indicated that the average nucleotide diversity of the panel was 1.21 × 10-4 for all sampled landraces. This average nucleotide diversity was 1.97 × 10-4, 1.01 × 10-4, and 1.89 × 10-4 for subgroups 1, 2, and 3, respectively. Genome-wide linkage disequilibrium (LD) analysis demonstrated that the average LD was about ∼8 kb. We evaluated 158 cassava varieties under 11 different environments. Finally, we identified 36 loci that were related to 11 agronomic traits by genome-wide association analyses. Four loci were associated with two traits, and 62 candidate genes were identified in the peak SNP sites. We found that 40 of these genes showed different expression profiles in different tissues. Of the candidate genes related to storage roots, Manes.13G023300, Manes.16G000800, Manes.02G154700, Manes.02G192500, and Manes.09G099100 had higher expression levels in storage roots than in leaf and stem; on the other hand, of the candidate genes related to leaves, Manes.05G164500, Manes.05G164600, Manes.04G057300, Manes.01G202000, and Manes.03G186500 had higher expression levels in leaves than in storage roots and stem. This study provides basis for research on genetics and the genetic improvement of cassava.
Highlights
IntroductionA crop introduced in China in the 1820s, is the main food consumed by approximately 600 million people in tropical and subtropical regions; this crop is the main material for starch and alcohol production (Balagopalan et al, 2001)
Cassava (Manihot esculenta Crantz, 2n = 36) is one of the three major tuberous crops produced worldwide
The Genome-wide association analysis (GWAS) on cassava landraces can be applied in simultaneous genetic mapping of multiple traits at a fine resolution
Summary
A crop introduced in China in the 1820s, is the main food consumed by approximately 600 million people in tropical and subtropical regions; this crop is the main material for starch and alcohol production (Balagopalan et al, 2001). GWAS of Agronomic Traits in Cassava heterozygous; its vegetative reproduction generates complex genetic background, which results in high genetic variability. Cassava was selectively domesticated at 7,000–12,000 years ago (Allem, 1994); its selective domestication yields the following characteristics: high mass accumulation, high starch rate, and the ability to grow and yield in unfavorable conditions, such as poor soil fertility and low rainfall. Molecular marker-assisted breeding is a feasible way to explore several beneficial allele variations through the selection of appropriate materials and desired phenotypic traits to locate desired functional genes or regions
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