Genome-wide identification of agronomically important genes in outcrossing crops using OutcrossSeq

Abstract

Many important crops (e.g., tuber, root, and tree crops) are cross-pollinating. For these crops, no inbred lines are available for genetic study and breeding because they are self-incompatible, clonally propagated, or have a long generation time, making the identification of agronomically important genes difficult, particularly in crops with a complex autopolyploid genome. In this study, we developed a method, OutcrossSeq, for mapping agronomically important loci in outcrossing crops based on whole-genome low-coverage resequencing of a large genetic population, and designed three computation algorithms in OutcrossSeq for different types of outcrossing populations. We applied OutcrossSeq to a tuberous root crop (sweet potato, autopolyploid), a tree crop (walnut tree, highly heterozygous diploid), and hybrid crops (double-cross populations) to generate high-density genotype maps for the outcrossing populations, which enable precise identification of genomic loci underlying important agronomic traits. Candidate causative genes at these loci were detected based on functional clues. Taken together, our results indicate that OutcrossSeq is a robust and powerful method for identifying agronomically important genes in heterozygous species, including polyploids, in a cost-efficient way. The OutcrossSeq software and its instruction manual are available for downloading at www.xhhuanglab.cn/tool/OutcrossSeq.html.

Polyploid QTL‐seq towards rapid development of tightly linked DNA markers for potato and sweetpotato breeding through whole‐genome resequencing

“…Yamamoto et al (2020) developed a low-coverage RADseq-based genotyping method, ngsAssocPoly, and detected loci associated with skin colour and internode length by calculating allele dosage probabilities. Chen et al (2021) created Outcross-ingSeq, in which 1807 F 1 progenies were barcoded and wholegenome resequenced with 1.5-time coverage for each individual to identify loci controlling vein colour, leaf shape and number of storage roots. These low-coverage NGS methods are costefficient but labour-intensive because the preparation of barcoded sequencing libraries is necessary for each progeny.…”

“…Chen et al. ( 2021 ) created OutcrossingSeq, in which 1807 F 1 progenies were barcoded and whole‐genome resequenced with 1.5‐time coverage for each individual to identify loci controlling vein colour, leaf shape and number of storage roots. These low‐coverage NGS methods are cost‐efficient but labour‐intensive because the preparation of barcoded sequencing libraries is necessary for each progeny.…”

Genotype calling and haplotype inference from low coverage sequence data in heterozygous plant genome using HetMap

“…One primary step of NGS data analysis is to do genotyping from the short reads data to generate the genome variation map. There are already some excellent pipelines like SNPtools (Wang et al 2013),GotCloud (Jun et al 2015) and OutcrossSeq (Chen et al 2021) that provide the whole work ow from raw sequence data to imputed genotype matrix. However, most populate software and pipelines are devoted to tackle the model species genome sequence data.…”

The Expression of IbMYB1 Is Essential to Maintain the Purple Color of Leaf and Storage Root in Sweet Potato [Ipomoea batatas (L.) Lam]

“…It provides a common model for understanding the genetic basis of color mutants ( Zhu et al, 2015 ; Sun et al, 2018 ). The co-expression network analysis (WGCNA) ( Langfelder and Horvath, 2008 ) and the knowledge-based identification of pathway enzymes (KIPEs) ( Pucker et al, 2020 ) based on the genome-wide and transcriptome-wide analyses have been applied to identify the tissue-specific regulation of anthocyanin biosynthesis ( Tombuloglu et al, 2013 ; Liu et al, 2018 , 2020 ; Iorizzo et al, 2020 ; Qin et al, 2020 ; Zhang et al, 2020 ; Chen et al, 2021 ; Parra-Galindo et al, 2021 ).…”

“…It has been confirmed that IbMYB1-2 plays a vital regulatory role in anthocyanin accumulation in storage roots ( Tanaka et al, 2011 ), but it is not necessary in all varieties for the expression of IbMYB1 ( Kim et al, 2010 ; Li et al, 2019 ; Zhang et al, 2020 ). A major locus of chromosome 5, where IbMYB1 genes are located, has been shown to have a large effect on the color variation of shoots ( Chen et al, 2021 ). We speculated that more IbMYB1 members with genetic complementation may be involved in the regulation of anthocyanin biosynthesis in cultivated species.…”