Genomic analyses provide insights into spinach domestication and the genetic basis of agronomic traits

Abstract

Spinach is a nutritious leafy vegetable belonging to the family Chenopodiaceae. Here we report a high-quality chromosome-scale reference genome assembly of spinach and genome resequencing of 305 cultivated and wild spinach accessions. Reconstruction of ancestral Chenopodiaceae karyotype indicates substantial genome rearrangements in spinach after its divergence from ancestral Chenopodiaceae, coinciding with high repeat content in the spinach genome. Population genomic analyses provide insights into spinach genetic diversity and population differentiation. Genome-wide association studies of 20 agronomical traits identify numerous significantly associated regions and candidate genes for these traits. Domestication sweeps in the spinach genome are identified, some of which are associated with important traits (e.g., leaf phenotype, bolting and flowering), demonstrating the role of artificial selection in shaping spinach phenotypic evolution. This study provides not only insights into the spinach evolution and domestication but also valuable resources for facilitating spinach breeding.

Genome-wide association study and genomic prediction of white rust resistance in USDA GRIN spinach germplasm

“…The publication of reference genomes and other new assemblies [ 15 – 19 ] has made genome-wide variant discovery in the germplasm panel and genome-wide association studies (GWAS) possible in spinach. With the decreasing genotyping cost in recent years and advanced statistical methods, GWAS and genomic selection (GS) approaches are commonly utilized to improve complex genetic traits in crops.…”

Genome-wide identification and expression analysis reveals spinach brassinosteroid-signaling kinase (BSK) gene family functions in temperature stress response

“…Under 37 °C/ 32 °C (day/night) treatment for 24 h, we found that the relative water content in leaves from heat- sensitive variety Sp73 was decreased to 66.1%, which was obviously lower than that in heat- tolerant variety Sp75 (75.7%) [ 3 , 4 ]. The genomics analysis on spinach presented a high-quality chromosome- scale reference genome, and the transcriptome sequencing and population genomic investigations discovered the genome architecture, evolution, and domestication, which was valuable for understanding the genetic basis of important agronomic traits and breeding [ 1 , 5 ]. Besides, high- throughput proteomics analysis on spinach varieties of Sp73 and Sp75 revealed that heat perception, signal transduction, and reactive oxygen species (ROS) scavenging were crucial for the heat tolerance [ 3 , 4 ].…”

“…In this study, seven members of the spinach BSK gene family were identified by screening the spinach whole- genome database [ 1 , 5 ]. The phylogenetic trees were constructed along with their homologous genes from sugar beet ( Beta vulgaris ), Arabidopsis, rice, maize, as well as common tobacco ( Nicotiana tabacum ) and woodland tobacco ( Nicotiana sylvestris ) for evaluating the evolution relationship and classification.…”

Chromosome-Scale, Haplotype-Resolved Genome Assembly of Suaeda Glauca

“…With the advent of the genome era, Beta vulgaris ( Rodríguez del Río et al, 2019 ), Spinacia oleracea ( Cai et al, 2021 ), and Chenopodium quinoa ( Jarvis et al, 2017 ) of the Amaranthaceae plants, have been sequenced and assembled high-quality genomes. The evolution of the Amaranthaceae genomes is very complex, and their karyotypes and genome size differ greatly ( Cai et al, 2021 ). Complete assemblies for Suaeda glauca mitochondria (474,330 bp) and chloroplast (149,807 bp) have been published ( Qu et al, 2019 ; Cheng Y. et al, 2021 ).…”