QTL Analysis of Head Splitting Resistance in Cabbage (Brassica oleracea L. var. capitata) Using SSR and InDel Makers Based on Whole-Genome Re-Sequencing.

Yanbin Su,Yangyong Zhang,Yumei Liu,Zhiyuan Fang,Zhansheng Li,Limei Yang,Mu Zhuang,Pawan L Kulwal

doi:10.1371/journal.pone.0138073

Yanbin Su, Yangyong Zhang + Show 6 more

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https://doi.org/10.1371/journal.pone.0138073

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Abstract

Head splitting resistance (HSR) in cabbage is an important trait closely related to both quality and yield of head. However, the genetic control of this trait remains unclear. In this study, a doubled haploid (DH) population derived from an intra-cross between head splitting-susceptible inbred cabbage line 79–156 and resistant line 96–100 was obtained and used to analyze inheritance and detect quantitative trait loci (QTLs) for HSR using a mixed major gene/polygene inheritance analysis and QTL mapping. HSR can be attributed to additive-epistatic effects of three major gene pairs combined with those of polygenes. Negative and significant correlations were also detected between head Hsr and head vertical diameter (Hvd), head transverse diameter (Htd) and head weight (Hw). Using the DH population, a genetic map was constructed with simple sequence repeat (SSR) and insertion–deletion (InDel) markers, with a total length of 1065.9 cM and average interval length of 4.4 cM between adjacent markers. Nine QTLs for HSR were located on chromosomes C3, C4, C7, and C9 based on 2 years of phenotypic data using both multiple-QTL mapping and inclusive composite interval mapping. The identified QTLs collectively explained 39.4 to 59.1% of phenotypic variation. Three major QTLs (Hsr 3.2, 4.2, 9.2) showing a relatively larger effect were robustly detected in different years or with different mapping methods. The HSR trait was shown to have complex genetic mechanisms. Results from QTL mapping and classical genetic analysis were consistent. The QTLs obtained in this study should be useful for molecular marker-assisted selection in cabbage breeding and provide a foundation for further research on HSR genetic regulation.

Highlights

Cabbage (Brassica oleracea L. var. capitata) is of immense importance for human nutrition, providing dietary fiber, vitamins, and cancer-preventing substances [1,2], and is one of the world’s most widely cultivated vegetables
A doubled haploid (DH) population derived from an intra-cross between head splitting-susceptible inbred cabbage line 79–156 and resistant line 96–100 was obtained and used to analyze inheritance and detect quantitative trait loci (QTLs) for Head splitting resistance (HSR) using a mixed major gene/polygene inheritance analysis and quantitative trait locus (QTL) mapping
Nine QTLs for HSR were located on chromosomes C3, C4, C7, and C9 based on 2 years of phenotypic data using both multiple-QTL mapping and inclusive composite interval mapping

Summary

Introduction

Cabbage (Brassica oleracea L. var. capitata) is of immense importance for human nutrition, providing dietary fiber, vitamins, and cancer-preventing substances [1,2], and is one of the world’s most widely cultivated vegetables. Farmers generally reduce irrigation times during late-stage cultivation. Such practices affect normal cabbage head growth, and cannot completely prevent head splitting. As for InDel markers, they are obtained with the massive re-sequencing data through bioinformatic methods and the electrophoresis bands are more credible with single distinguishable bands of about 100–200 bp, which reduces the genotyping errors greatly [27]. We located the QTLs for HSR on the generated linkage map and analyzed QTL stability across years with different mapping programs This information may increase the understanding on the genetic base and molecular mechanism of HSR trait and it is useful in order to identify genes controlling HSR in cabbage

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