Identification of Functional Single-Nucleotide Polymorphisms Affecting Leaf Hair Number in Brassica rapa.

Wenting Zhang,Xiaorong Li,Shirin Mirlohi,Yuke He

doi:10.1104/pp.18.00025

Abstract

Leaf traits affect plant agronomic performance; for example, leaf hair number provides a morphological indicator of drought and insect resistance. Brassica rapa crops have diverse phenotypes, and many B. rapa single-nucleotide polymorphisms (SNPs) have been identified and used as molecular markers for plant breeding. However, which SNPs are functional for leaf hair traits and, therefore, effective for breeding purposes remains unknown. Here, we identify a set of SNPs in the B. rapa ssp. pekinenesis candidate gene BrpHAIRY LEAVES1 (BrpHL1) and a number of SNPs of BrpHL1 in a natural population of 210 B. rapa accessions that have hairy, margin-only hairy, and hairless leaves. BrpHL1 genes and their orthologs and paralogs have many SNPs. By intensive mutagenesis and genetic transformation, we selected the functional SNPs for leaf hairs by the exclusion of nonfunctional SNPs and the orthologous and paralogous genes. The residue tryptophan-92 of BrpHL1a was essential for direct interaction with GLABROUS3 and, thus, necessary for the formation of leaf hairs. The accessions with the functional SNP leading to substitution of the tryptophan-92 residue had hairless leaves. The orthologous BrcHL1b from B. rapa ssp. chinensis regulates hair formation on leaf margins rather than leaf surfaces. The selected SNP for the hairy phenotype could be adopted as a molecular marker for insect resistance in Brassica spp. crops. Moreover, the procedures optimized here can be used to explain the molecular mechanisms of natural variation and to facilitate the molecular breeding of many crops.

Highlights

The genus Brassica is one of the most important branches of the Brassicaceae family, including many varieties of common vegetable crops
Some studies report that the leaf hairs in Chinese cabbage are controlled by a single dominant gene, whereas others have shown that leaf hairs are a quantitative phenotype, controlled by several major QTLs (Song et al, 1995; Zhang et al, 2009)
Bre is a representative of the allhairy phenotype and Wut is a representative of the margin-only hairy phenotype: numerous hairs were detected on the leaf surface and leaf margins of Bre, whereas only a few leaf hairs were seen on the leaf margins of Wut (Fig. 1, A and B)

Summary

Introduction

The genus Brassica is one of the most important branches of the Brassicaceae family, including many varieties of common vegetable crops. By means of natural and artificial selection through time, many crops in Brassica rapa have evolved that show obvious differences in leaf traits, such as heading Chinese cabbage The density and localization of leaf hairs vary with crops within B. rapa. Functional SNPs for Leaf Hair Number means for estimating the framework of the genetic architecture for a trait and potentially identifying the genes responsible for a specific phenotype. Four recombinant inbred mapping populations based on six Arabidopsis ecotypes have been used to reveal QTLs controlling trichome density, and nine QTLs have been identified as responsible for trichome initiation and development (Symonds et al, 2005). The mechanisms of trichome development in Brassica spp. crops and in Arabidopsis might be highly conserved (Nayidu et al, 2014; Alahakoon et al, 2016). A 5-bp deletion in Brtri (BrGL1) is related to a glabrous phenotype (Ye et al, 2016)

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