Portrait of a genus: the genetic diversity ofZea

Abstract

Maize is a globally valuable commodity and one of the most extensively studied genetic model organisms. However, we know surprisingly little about the extent and potential utility of the genetic variation found in the wild relatives of maize. Here, we characterize a high-density genomic variation map from ~700 genomes encompassing maize and all wild taxa of the genus Zea, identifying over 65 million single nucleotide polymorphisms (SNPs), 8 million Insertion/Deletion (InDel) polymorphisms, and over one thousand novel inversions. The variation map reveals evidence of selection within taxa displaying novel adaptations such as perenniality and regrowth. We focus in detail on evidence of convergent adaptation in highland teosinte and temperate maize. This study not only indicates the key role of hormone related pathways in highland adaptation and flowering time related pathways in high latitude adaptation, but also identifies significant overlap in the genes underlying adaptations to both environments. To show how this data can identify useful genetic variants, we generated and characterized novel mutant alleles for two flowering time candidate genes. This work provides the most extensive sampling to date of the genetic diversity inherent in the genus Zea, resolving questions on evolution and identifying adaptive variants for direct use in modern breeding.

Differences in activity and stability drive transposable element variation in tropical and temperate maize

“…mexicana genome were identified when a single blast hit covering ≥80% of the query with ≥95% identity was found in the genome. An age cutoff of ≤20 kya was also used to identify syntenic LTR-RTs that were inserted after the divergence between cultivated maize and its wild progenitor teosinte 68 and compared to the Zea mays ssp. mexicana- based polarization.…”

A pan-Zea genome map for enhancing maize improvement

“…The pan-Zea genome was constructed from the alignments against the maize B73 reference genome V4 (AGPv4) of the de novo draft assemblies from 721 individuals, including 507 diverse maize inbred lines [42], 31 landrace individuals [43], and 183 teosinte individuals [44]. An additional 11 chromosome-level assemblies of the Zea genus from previous studies were also included (Additional file 1: Fig.…”

“…The 691 pan-Zea individuals were divided into three maize sub-populations and eight teosinte sub-populations (Fig. 2B and C, [42,44]). To investigate whether these sub-populations lost genes and orthologous groups evenly, we clustered the dispensable genes into 16 clusters (CLS1-16 in Fig.…”

“…SVs have received significant attention and are responsible for various complex traits in many species [13,18,56]. Previous research has constructed a high-density haplotype map of the genus Zea using the same populations by mapping with the B73 reference genome [44]. To complement the genetic variation map and estimate the impact of SVs on the maize phenotypic variations, we constructed a comprehensive SV map by integrating evidences from variant graphs, comparative genomics, and short-read alignments.…”

Water stress resilient cereal crops: Lessons from wild relatives

“…Column next to the tree depicts genome composition of the species. Tree built with information from Petersen et al (2006), Wang et al (2011), Stein et al (2018), Haas et al (2019), Shenton et al (2020), Chen et al (2021), Fu (2021), and http://plants.ensembl.org.…”