Transposable element insertion: a hidden major source of domesticated phenotypic variation in Brassica rapa

Abstract

Transposable element (TE) is prevalent in plant genomes. However, studies on their impact on phenotypic evolution in crop plants are relatively rare, because systematically identifying TE insertions within a species has been a challenge. Here, we present a novel approach for uncovering TE insertion polymorphisms (TIPs) using pan-genome analysis combined with population-scale resequencing, and we adopt this pipeline to retrieve TIPs in a Brassica rapa germplasm collection. We found that 23% of genes within the reference Chiifu-401-42 genome harbored TIPs. TIPs tended to have large transcriptional effects, including modifying gene expression levels and altering gene structure by introducing new introns. Among 524 diverse accessions, TIPs broadly influenced genes related to traits and acted a crucial role in the domestication of B. rapa morphotypes. As examples, four specific TIP-containing genes were found to be candidates that potentially involved in various climatic conditions, promoting the formation of diverse vegetable crops in B. rapa. Our work reveals the hitherto hidden TIPs implicated in agronomic traits and highlights their widespread utility in studies of crop domestication.

Chromosome-scale genome assemblies of five differentBrassica oleraceamorphotypes provide insights in intraspecific diversification

“…The genealogical relationships within B. oleracea were consistent with morphotypes rather than geographical origin. The B. rapa lineage in our analysis largely corroborated the one revealed by Cai et al (Cai et al, 2022b) with minor differences, both of which revealed five monophyletic groups for these diverse B. rapa morphotypes. Estimation of divergence times based on Bayesian inference using MCMCTree program suggested that intraspecific diversification for the sister species B. oleracea (~4.21 Mya) and B. rapa (~4.33 Mya) happened simultaneously and shortly after their speciation (~6.5 Mya) (Fig.…”

Remarkable Divergence of the Sex-Linked Region between Two Wild Spinach Progenitors, Spinacia turkestanica and Spinacia tetrandra

“…The genotypes of 63 Spinacia accessions based on TIPs on the sex chromosomes was determined, as described by Cai et al (2022) [ 31 ]. One sample (PI604780) was removed because of the high missing rate.…”

“…We estimated the genotypes of each Spinacia accession as described by Cai et al (2022) [ 31 ]. Specifically, we first defined each TE insertion sequence and their 1 kb upstream and downstream as the TE reference.…”

“…The Y-TIPs (median length = 2776 bp) appeared longer than the X-TIPs (median length = 898 bp) in the SLR (Student's t-test, p = 0.0002) (Figure 3c). The genotypes of 63 Spinacia accessions based on TIPs on the sex chromosomes was determined, as described by Cai et al (2022) [31]. One sample (PI604780) was removed because of the high missing rate.…”

Root Breeding in the Post-Genomics Era: From Concept to Practice in Apple

“…Furthermore, β-carotene-derived retinoid plays important roles in circadian clock oscillation, neurogenesis, and vasculature development in animal cells. Recent studies found that retinol also mediates circadian clock oscillations and regulates the development of plant lateral roots in plant cells [ 162 ].…”