Eight soybean reference genome resources from varying latitudes and agronomic traits

Jeffrey Shih-Chieh Chu,Huan Wang,Guang Li,Huangkai Zhou,Xianzhong Feng,Bo Peng,Jiantian Leng,Kuanqiang Tang,Xingxing Yi,Nansheng Chen

doi:10.1038/s41597-021-00947-2

Abstract

Comparative analysis of multiple reference genomes representing diverse genetic backgrounds is critical for understanding the role of key alleles important in domestication and genetic breeding of important crops such as soybean. To enrich the genetic resources for soybean, we describe the generation, technical assessment, and preliminary genomic variation analysis of eight de novo reference-grade soybean genome assemblies from wild and cultivated accessions. These resources represent soybeans cultured at different latitudes and exhibiting different agronomical traits. Of these eight soybeans, five are from new accessions that have not been sequenced before. We demonstrate the usage of these genomes to identify small and large genomic variations affecting known genes as well as screening for genic PAV regions for identifying candidates for further functional studies.

Highlights

Background & SummarySoybean is an important crop that is responsible for about 50% of the world’s oilseed production, and a source of high-quality protein for animal feeds
Recent genomic advances in many plant and animal species have shown that a single reference genome is insufficient to capture and represent the variations that exist within the population of the corresponding species[4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20]
Resequencing and de novo assembly of wild and cultivated soybean accessions identified hundreds of genic presence-absence variations (PAVs) or SVs affecting agronomic genes compared to Williams 82 (W82) genome[7,21,22,23,24,25,26]

Summary

Introduction

Background & SummarySoybean is an important crop that is responsible for about 50% of the world’s oilseed production (www.fao.org), and a source of high-quality protein for animal feeds. Resequencing and de novo assembly of wild and cultivated soybean accessions identified hundreds of genic presence-absence variations (PAVs) or SVs affecting agronomic genes compared to W82 genome[7,21,22,23,24,25,26]. We report the sequencing, genome assembly, annotation, and genomic variation resources generated for the assembly of 8 reference-grade soybean genomes.

Results

Conclusion