Targeted Sequencing of the Short Arm of Chromosome 6V of a Wheat Relative Haynaldia villosa for Marker Development and Gene Mining

Xu Zhang,Mengli Li,Wentao Wan,Haiyan Wang,Xiue Wang,Jaroslav Doležel,Jan Vrána,Zhongyu Yu,Yufeng Wu,Jia Liu,Jin Xiao,Kateřina Holušová

doi:10.3390/agronomy11091695

Abstract

The short arm of chromosome 6V (6VS) of Haynaldia villosa has been used in wheat breeding programs to introduce Pm21 resistance gene against powdery mildew (Pm) and some other genes. In this this study, 6VS was flow-sorted from wheat-H. villosa ditelosomic addition line Dt6VS and sequenced by Illumina technology. An assembly of 230.39 Mb was built with contig N50 of 9.788 bp. In total, 3.276 high-confidence genes were annotated and supported by RNA sequencing data. Repetitive elements represented 74.91% of the 6VS assembly. The 6VS homologous genes were identified on homologous group 6 in six Triticeae species confirming their synteny relationships. Out of 45 NB-ARC domain proteins identified on 6VS, 15 were upregulated and might also be involved in the innate immunity of H. villosa to Pm. High thousand grain weight (TGW) for 6VS/6AL translocation line was not attributable to GW2-6V gene. Based on the intron size differences, 119 intron-target (IT) markers were developed to trace the 6VS chromatins introduced into wheat background. The assembled 6VS genome sequence and the developed 6VS specific IT markers in this work will facilitate the gene mining and utilization of agronomic important genes on 6VS.

Highlights

Haynaldia villosa L. (2n = 14, genome villosa villosa (VV)), a wild relative of common wheat (Triticum aestivum L.), carries resistance genes to several wheat diseases, including powdery mildew, wheat yellow mosaic virus, eyespot, take-all and rusts [1]
Several useful genes were mapped on short arm of chromosome 6V, such as the Pm21 locus, which provides immunity or high resistance to all powdery mildew isolates, and NAM-V1, which contributes to increased grain protein content (GPC) in the wheat-H. villosa 6AL/6VS translocation lines [9,10]
Flow cytometric analysis of chromosomes isolated from T. aestivum–H. villosa 6VS

Summary

Introduction

(2n = 14, genome VV), a wild relative of common wheat (Triticum aestivum L.), carries resistance genes to several wheat diseases, including powdery mildew, wheat yellow mosaic virus, eyespot, take-all and rusts [1] It has been credited for improving tiller number [2,3], high grain protein content [4,5,6], and tolerances to frost and drought [7,8]. Several useful genes were mapped on short arm of chromosome 6V, such as the Pm21 locus, which provides immunity or high resistance to all powdery mildew isolates, and NAM-V1, which contributes to increased grain protein content (GPC) in the wheat-H. villosa 6AL/6VS translocation lines [9,10]. It simplifies bioinformatic analyses due to reduced volume of sequence data

Methods

Results

Discussion

Conclusion