Multi-environment QTL analysis delineates a major locus associated with homoeologous exchanges for water-use efficiency and seed yield in allopolyploidBrassica napus

Abstract

SummaryCanola varieties exhibit discernible variation in drought avoidance and drought escape traits, suggesting its adaptation to water-deficit environments. However, the underlying mechanisms are poorly understood.A doubled haploid (DH) population was analysed to identify QTL associated with water use efficiency (WUE) related traits. Based on the resequenced parental genome data, we developed sequence-capture based markers for fine mapping. mRNA-Seq was performed to determine the expression of candidate genes underlying QTL for carbon isotope discrimination (Δ13C).QTL contributing to main and QTL × Environment interaction effects for Δ13C and for agronomic WUE were identified. One multi-trait QTL for Δ13C, days to flower, plant height and seed yield was identified on chromosome A09, in the vicinity of ERECTA. Interestingly, this QTL region was overlapped with a homoeologous exchange event (HE), suggesting its association with the major QTL. Transcriptome analysis revealed several differentially expressed genes between parental lines, including in HE regions.This study provides insights into the complexity of WUE related genes in the context of canola adaptation to water-deficit conditions. Our results suggest that alleles for high Δ13C contribute positively to canola yield. Genetic and genomic resources developed herein could be utilised to make genetic gains for improving canola WUE.

Effects of homoeologous exchange on gene expression and alternative splicing in a newly formed allotetraploid wheat

“…For each homoeolog pair (three replicates), significance of cis + trans effects (‘a’, expression difference between orthologs A and D in the in silico mix of RNA‐seq data) and cis ‐effects (‘b’, expression divergence between homoeologs A and D in the sibling HE‐free tetraploid plants) were determined by DESeq2 (see ‘Analysis of homoeolog pairs’ in the Experimental Procedures section). The trans ‐effect (‘a − b’, log 2 ‐transformed A:D ratio between the in silico mix and the sibling HE‐free [except for a single shared HE] tetraploid plants) was tested through Student's t ‐test and the P ‐values were then corrected by the FDR method with rate of 0.05 (Raman et al., 2021). In total, 8035 expressed homoeolog pairs were classified into six groups: (i) cis only: significant difference in ‘b’ but not in ‘a − b’; (ii) trans only: significant difference in both ‘a’ and ‘a − b’ but not in ‘b’; (iii) compensatory: significant difference in both ‘b’ and ‘a − b’ but not in ‘a’; (iv) cis and trans : significant difference in ‘a’, ‘b’ and ‘a − b’; (v) conserved: no significant difference in ‘a’, ‘b’ and ‘a − b’; and (vi) ambiguous: homoeolog pairs that did not meet any of the above criteria.…”

“…In total, 13 468 homoeolog pairs were identified by jcvi utility libraries (https://github.com/tanghaibao/jcvi) based on sequence similarity and the genomic position of genes from subgenomes A and D. To identify HEB, DESeq2 was performed to compare the expression difference between members of each homoeolog pair in both the in silico mix (merging two parental RNA‐seq data at 1:1 ratio) and the sibling HE‐free (except for a single shared HE) tetraploid plants using the read count data of three replicates (Chalhoub et al., 2014; Raman et al., 2021). Homoeolog pairs with q < 0.05 and TPM fold change > 2 were defined as biased expression (A‐bias or D‐bias).…”

“…This suggests HE‐underpinned genetic variants have been selected for during domestication and crop improvement. Indeed, it was documented that HE confers high adaptability and generates a wide range of morphophysiological variations desired in crops (Pires et al., 2004; Raman et al., 2021; Shi et al., 2021; Stein et al., 2017). It was also posited that under natural settings HE plays important parts in generating major evolutionary novelty, accelerating diploidization and facilitating species diversification (Edger et al., 2018; Mason & Wendel, 2020).…”