Genome-Wide Association Studies of 11 Agronomic Traits in Cassava (Manihot esculenta Crantz)

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.

Seasonal Variation in Starch Accumulation and Starch Granule Size in Cassava Genotypes in a Tropical Savanna Climate

“…Based on molecular techniques, archaeological evidence and fossil remains, the domestication of cassava (Manihot esculenta Crantz, 2n = 36) traced back to about 7000 to 12,000 years ago, and their selection by ancient farmers and modern plant breeders resulted in the modern cassava cultivars with extraordinary characteristics including a high biomass and high starch yield, high ability to grow in unfavorable environments, and tolerance to drought [1]. Nowadays, cassava contributes significantly to the nutrition and livelihood of up to 800 million people worldwide [2].…”

Genome-wide association analysis of fiber fineness and yield in ramie (Boehmeria nivea) using SLAF-seq

“…Here, the genome-wide LD decayed to r 2 = 0.1 was 11.75 kb in physical distance. This value was substantially lower than those for most other crops such as rice (Oryza sativa L.) (167 kb) [31], soybean (420 kb) [32], and cultivated maize (Zea mays L.) (30 kb) [33], but higher than that of cultivated cassava (Manihot esculenta L.) (8 kb) [34], inbred maize (Zea mays L.) (1.5 kb) [35], and inbred potato (Solanum tuberosum L.) (1 kb) [36]. Therefore, the 112 ramie accessions of the present study should have abundant allelic diversity based on the rapid LD decay in most of the scaffolds.…”

Modernising breeding for orphan crops: tools, methodologies, and beyond

“…The African Orphan Crops Consortium (AOCC, http://afric anorp hancr ops.org/), for instance, is working on sequencing 101 traditional African food crops, adding to the list of more than 700 plant species that have already been sequenced according to the US National Center for Biotechnology Information (NCBI, https ://www.ncbi.nlm.nih.gov/genom e/). The increasing number of diversity panels of orphan crops that have been genotyped using next-generation sequencing (NGS) or highdensity SNP arrays opens new perspectives on unlocking these challenging breeding traits through genome-wide association studies (Upadhyaya 2015;Xu et al 2017;Zhang et al 2018) or high resolution mapping in multi-parent advanced generation intercross (MAGIC) populations (Herniter et al 2018;Ongom and Ejeta 2018).…”