Chromosome evolution and the genetic basis of agronomically important traits in greater yam

Abstract

The nutrient-rich tubers of the greater yam Dioscorea alata L. provide food and income security for millions of people around the world. Despite its global importance, however, greater yam remains an "orphan crop." Here we address this resource gap by presenting a highly-contiguous chromosome-scale genome assembly of greater yam combined with a dense genetic map derived from African breeding populations. The genome sequence reveals an ancient lineage-specific genome duplication, followed by extensive genome-wide reorganization. Using our new genomic tools we find quantitative trait loci for susceptibility to anthracnose, a damaging fungal pathogen of yam, and several tuber quality traits. Genomic analysis of breeding lines reveals both extensive inbreeding as well as regions of extensive heterozygosity that may represent interspecific introgression during domestication. These tools and insights will enable yam breeders to unlock the potential of this staple crop and take full advantage of its adaptability to varied environments.

Identification of QTLs Controlling Resistance to Anthracnose Disease in Water Yam (Dioscorea alata)

“…Cutadapt 1.2.1 [ 36 ] was used to remove the adaptors and low-quality bases read with a mean quality score <30 using a free perl script , accessed on 11 March 2020. For the final SNP calling, GATK was used while mapping was performed using default options of Burrows-Wheeler Aligner (BWA) [ 37 ] using the D. alata reference genome v2.1 [ 38 ]. The SNP quality assessment was performed using vcftools [ 39 ] and plink [ 40 ].…”

“…Markers linked with the yam anthracnose disease were then placed in the respective chromosome, and their position was viewed using Qtl/jittermap. For the gene mining, the related putative genes associated with SNP markers were searched within the upstream and downstream locations of the QTL generic feature format (GFF3) of the reference genome of D. alata v2.1 [ 38 ] available on , accessed 1 May 2021. Functions of the different genes associated with the identified QTL were determined using the public database Interpro, European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI).…”

Rhizophagus irregularis and nitrogen fixing azotobacter enhances greater yam (Dioscorea alata) biochemical profile and upholds yield under reduced fertilization

“…The chromosome number of D. alata is varied from 2n = 40,60,80; that’s why it is called the polyploid spp. ( Bredeson et al, 2021 ). Consequently, the importance of greater yam in food security has crossed several genetic improvement programs intending to develop new varieties with a higher yield ( Arnau et al, 2017 ).…”

Homing in on Endogenous Badnaviral Elements: Development of Multiplex PCR-DGGE for Detection and Rapid Identification of Badnavirus Sequences in Yam Germplasm

“…Access to the D. rotundata ( Tamiru et al, 2017 ) and D. alata genomes ( Bredeson et al, 2021 ) published in recent years will facilitate the study of eDBVs in yam, their potential allelic structures, and the dating of eDBV insertion events, as discussed by Umber et al (2014) . To date, it cannot be ruled out that infectious eDBVs exist in yam genomes and access to increasing numbers of complete annotated yam genomes will hopefully shed light into the possible impact of eDBVs on yam breeding and multiplication programmes.…”