Construction of a High-Density Genetic Map Based on SLAF Markers and QTL Analysis of Leaf Size in Rice.

Yi Wen,Qiang Zhang,Dali Zeng,Guojun Dong,Dawei Xue,Longbiao Guo,Qian Qian,Hao Wu,Jiang Hu,Guang Chen,Guangheng Zhang,Lan Shen,Deyong Ren,Yueying Wang,Yiqing Tan,Yunxia Fang,Zhenyu Gao,Li Zhu,Linlin Hou,Peng Hu,Xing‐Wang Deng

doi:10.3389/fpls.2020.01143

Abstract

Leaf shape is an important agronomic trait for constructing an ideal plant type in rice, and high-density genetic map is facilitative in improving accuracy and efficiency for quantitative trait loci (QTL) analysis of leaf trait. In this study, a high-density genetic map contained 10,760 specific length amplified fragment sequencing (SLAF) markers was established based on 149 recombinant inbred lines (RILs) derived from the cross between Rekuangeng (RKG) and Taizhong1 (TN1), which exhibited 1,613.59 cM map distance with an average interval of 0.17 cM. A total of 24 QTLs were detected and explained the phenotypic variance ranged from 9% to 33.8% related to the leaf morphology across two areas. Among them, one uncloned major QTL qTLLW1 (qTLL1 and qTLLW1) involved in regulating leaf length and leaf width with max 33.8% and 22.5% phenotypic variance respectively was located on chromosome 1, and another major locus qTLW4 affecting leaf width accounted for max 25.3% phenotypic variance was mapped on chromosome 4. Fine mapping and qRT-PCR expression analysis indicated that qTLW4 may be allelic to NAL1 (Narrow leaf 1) gene.

Highlights

Most important agronomic traits are quantitatively inherited, and generally controlled or affected by multiple quantitative trait loci (QTL)
A total of 47 Gb data containing 211,574,337 reads were obtained by high throughput sequencing, and average Q30 and GC content were 92.54% and 43.54%, respectively (Table 1). These reads were aligned to the reference rice genome via BurrowsWheeler Alignment (BWA) software (Li et al, 2009), and the single locus without repetition was considered as a valid SLAF locus
78,374 polymorphic SLAFs were identified and accounted for 32.13% of total 243,955 SLAFs (Supplementary Table S3). These SLAFs were evenly distributed on 12 chromosomes (Figure 1) and 63,538 SLAFs were successfully genotyped according to the general twoelement genotype coding rules of genetics

Summary

Introduction

Most important agronomic traits are quantitatively inherited, and generally controlled or affected by multiple quantitative trait loci (QTL). Through sequencing of SLAF-seq library constructed by genomic DNA of special enzyme digestion, the polymorphic SLAFs obtained from difference sequence analysis. Each SLAF locus corresponds to a specific fragment generated by enzyme digestion, which includes difference sites of insertion-deletion (InDel) and SNP (Sun et al, 2013). The technology enables us to obtain enough polymorphic markers to carry out QTL mapping and markerassisted selection (MAS), and exhibits several advantages than conventional molecular markers, including rich polymorphism, uniform distribution, avoiding repeated sequences, not missing important regions of chromosome segment, low cost, short cycle and so on (Sun et al, 2013; Chang et al, 2018). SLAFseq has been widely and successfully applied for genetic map construction and QTL analysis in multiple species (Chen et al, 2013; Li et al, 2014; Zhu et al, 2016; Yin et al, 2018; Zhu et al, 2018; Wu et al, 2019; Yu et al, 2019)

Methods

Results

Discussion

Conclusion