A high-density SNP genetic map consisting of a complete set of homologous groups in autohexaploid sweetpotato (Ipomoea batatas)

Abstract

Sweetpotato (Ipomoea batatas) is an autohexaploid species with 90 chromosomes (2n = 6x = 90) and a basic chromosome number of 15, and is therefore regarded as one of the most challenging species for high-density genetic map construction. Here, we used single nucleotide polymorphisms (SNPs) identified by double-digest restriction site-associated DNA sequencing based on next-generation sequencing technology to construct a map for sweetpotato. We then aligned the sequence reads onto the reference genome sequence of I. trifida, a likely diploid ancestor of sweetpotato, to detect SNPs. In addition, to simplify analysis of the complex genetic mode of autohexaploidy, we used an S1 mapping population derived from self-pollination of a single parent. As a result, 28,087 double-simplex SNPs showing a Mendelian segregation ratio in the S1 progeny could be mapped onto 96 linkage groups (LGs), covering a total distance of 33,020.4 cM. Based on the positions of the SNPs on the I. trifida genome, the LGs were classified into 15 groups, each with roughly six LGs and six small extra groups. The molecular genetic techniques used in this study are applicable to high-density mapping of other polyploid plant species, including important crops.

Genome‐wide association studies on the phyllosphere microbiome: Embracing complexity in host–microbe interactions

“…As more diverse genomes are included in a panel and LD decreases, a denser set of SNPs will be necessary to ensure that all the relevant variants in the genome fall within the LD block of a marker. High‐density SNP panels already exist for a variety of plant species (Bayer et al ., ; Shirasawa et al ., ; Eltaher et al ., ).…”

Genetic mapping in polyploids

“…Examples of allopolyploid SNP arrays include cotton (Hulse-Kemp et al, 2015), oat (Tinker et al, 2014), oilseed rape (Dalton- Morgan et al, 2014;Clarke et al, 2016), peanut (Pandey et al, 2017), strawberry (Bassil et al, 2015) and wheat (Akhunov et al, 2009;Cavanagh et al, 2013;Wang et al, 2014b;Winfield et al, 2016). Untargeted approaches such as genotyping-by-sequencing have also been applied, for example in autopolyploids such as alfalfa Yu et al, 2017), blueberry (McCallum et al, 2016), bluestem prairie grass (Andropogon gerardii) (McAllister and Miller, 2016), cocksfoot (Dactylis glomerata) (Bushman et al, 2016), potato (Uitdewilligen et al, 2013;Sverrisdóttir et al, 2017), sugarcane (Balsalobre et al, 2017;Yang et al, 2017b) and sweet potato (Shirasawa et al, 2017), and in allopolyploids such as coffee (Moncada et al, 2016), cotton (Islam et al, 2015;Reddy et al, 2017), intermediate wheatgrass (Thinopyrum intermedium) (Kantarski et al, 2017), oat (Chaffin et al, 2016), prairie cordgrass (Spartina pectinata) (Crawford et al, 2016), shepherd's purse (Capsella bursa-pastoris) (Cornille et al, 2016), wheat (Poland et al, 2012;Edae et al, 2015) and zoysiagrass (Zoysia japonica) (McCamy et al, 2018) (noting that the precise classification of some of these species as auto-or allopolyploids has yet to be conclusively determined). Whatever the technology used, it is clear that we are currently witnessing an explosion of interest in polyploid genomics.…”

“…Homologue-specific maps are still regularly generated in polyploid mapping studies (e.g. in potato , rose (Vukosavljev et al, 2016) or sweet potato (Shirasawa et al, 2017)), for which LPmerge (or a similarly-efficient integration algorithm) could then be used to generate chromosomally-integrated maps.…”

“…In this species, several non-integrated maps have been published (Ukoskit and Thompson, 1997;Kriegner et al, 2003;Cervantes-Flores et al, 2008;Chang et al, 2009;Monden et al, 2015;Shirasawa et al, 2017), with three publications reporting information on homologous chromosomes without actually integrating the maps. In two publications, this information was based on markers that had a dosage of two (duplex) in one parent and zero (nulliplex) in the other (2x0 markers), and markers with a dosage three (triplex) in one parent and zero in the other (3x0 markers; (Ukoskit and Thompson, 1997;Cervantes-Flores et al, 2008)).…”

“…In two publications, this information was based on markers that had a dosage of two (duplex) in one parent and zero (nulliplex) in the other (2x0 markers), and markers with a dosage three (triplex) in one parent and zero in the other (3x0 markers; (Ukoskit and Thompson, 1997;Cervantes-Flores et al, 2008)). Others have identified homologous chromosomes based on alignment to a reference genome (Shirasawa et al, 2017). Similar to sweet potato, chrysanthemum is an outcrossing hexaploid with polysomic inheritance (van Geest et al, 2017c).…”