Genome-Wide DNA Polymorphism Analysis and Molecular Marker Development for the Setaria italica Variety "SSR41" and Positional Cloning of the Setaria White Leaf Sheath Gene SiWLS1.

Hui Zhang,Yuanzhu Gao,Qiang He,Baili Feng,Xianmin Diao,Guanqing Jia,James C Schnable,Mingzhao Luo,Sha Tang,Hui Zhi

doi:10.3389/fpls.2021.743782

Abstract

Genome-wide DNA polymorphism analysis and molecular marker development are important for forward genetics research and DNA marker-assisted breeding. As an ideal model system for Panicoideae grasses and an important minor crop in East Asia, foxtail millet (Setaria italica) has a high-quality reference genome as well as large mutant libraries based on the “Yugu1” variety. However, there is still a lack of genetic and mutation mapping tools available for forward genetics research on S. italica. Here, we screened another S. italica genotype, “SSR41”, which is morphologically similar to, and readily cross-pollinates with, “Yugu1”. High-throughput resequencing of “SSR41” identified 1,102,064 reliable single nucleotide polymorphisms (SNPs) and 196,782 insertions/deletions (InDels) between the two genotypes, indicating that these two genotypes have high genetic diversity. Of the 8,361 high-quality InDels longer than 20 bp that were developed as molecular markers, 180 were validated with 91.5% accuracy. We used “SSR41” and these developed molecular markers to map the white leaf sheath gene SiWLS1. Further analyses showed that SiWLS1 encodes a chloroplast-localized protein that is involved in the regulation of chloroplast development in bundle sheath cells in the leaf sheath in S. italica and is related to sensitivity to heavy metals. Our study provides the methodology and an important resource for forward genetics research on Setaria.

Highlights

Foxtail millet (Setaria italica) and its wild ancestor green foxtail (Setaria viridis) are annual diploid grass species
Previous studies have developed a number of simple sequence repeat (SSR) and single nucleotide polymorphisms (SNPs) markers that can be used for genotyping different foxtail millet accessions (Jia et al, 2013; Zhang et al, 2014)
In the F2 generation, the segregation ratio of plants with a green leaf sheath (745 individuals) and those with a white leaf sheath (237 individuals) was close to 3:1 (Supplementary Table 8). These results clearly indicated that the white leaf sheath phenotype is controlled by a single recessive nuclear gene

Summary

INTRODUCTION

Foxtail millet (Setaria italica) and its wild ancestor green foxtail (Setaria viridis) are annual diploid grass species. Setaria italica has many distinctive characteristics, including (i) C4 photosynthesis and tolerance to drought and low-quality soils; (ii) small, high-quality reference genomes (Bennetzen et al, 2012), with well-organized bioinformatic databases; (iii) a short lifespan, the ability to self-pollinate, and prolific seed production; (iv) easy management in the laboratory ( grown in growth chambers, no-seed shattering, and short seed dormancy) Because of these advantages, Setaria has been proposed as a molecular genetic model plant for C4 biology and for crop functional genomics analyses (Diao et al, 2014). More than 8,000 genome-wide molecular markers were developed, and 180 of them were validated by PCR Using these newly developed markers, we mapped the novel white leaf sheath gene SiWLS1 encoding a chloroquine-resistance transporter in foxtail millet by positional cloning. Our research provides useful genome resources for gene cloning and molecular breeding of foxtail millet and will be useful for the further development of Setaria as a model system

MATERIALS AND METHODS

RESULTS

DISCUSSION

Findings

DATA AVAILABILITY STATEMENT