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QTL Landscape for Oil Content in Brassica juncea: Analysis in Multiple Bi-Parental Populations in High and “0” Erucic Background

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      Abstract

      Increasing oil content in oilseed mustard ( Brassica juncea) is a major breeding objective—more so, in the lines that have “0” erucic acid content (< 2% of the seed oil) as earlier studies have shown negative pleiotropic effect of erucic acid loci on the oil content, both in oilseed mustard and rapeseed. We report here QTL analysis of oil content in eight different mapping populations involving seven different parents—including a high oil content line J8 (~49%). The parental lines of the mapping populations contained wide variation in oil content and erucic acid content. The eight mapping populations were categorized into two sets—five populations with individuals segregating for erucic acid (SE populations) and the remaining three with zero erucic acid segregants (ZE populations). Meta-analysis of QTL mapped in individual SE populations identified nine significant C-QTL, with two of these merging most of the major oil QTL that colocalized with the erucic acid loci on the linkage groups A08 and B07. QTL analysis of oil content in ZE populations revealed a change in the landscape of the oil QTL compared to the SE populations, in terms of altered allelic effects and phenotypic variance explained by ZE QTL at the “common” QTL and observation of “novel” QTL in the ZE background. The important loci contributing to oil content variation, identified in the present study could be used in the breeding programmes for increasing the oil content in high erucic and “0” erucic backgrounds.

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      Empirical threshold values for quantitative trait mapping.

      The detection of genes that control quantitative characters is a problem of great interest to the genetic mapping community. Methods for locating these quantitative trait loci (QTL) relative to maps of genetic markers are now widely used. This paper addresses an issue common to all QTL mapping methods, that of determining an appropriate threshold value for declaring significant QTL effects. An empirical method is described, based on the concept of a permutation test, for estimating threshold values that are tailored to the experimental data at hand. The method is demonstrated using two real data sets derived from F(2) and recombinant inbred plant populations. An example using simulated data from a backcross design illustrates the effect of marker density on threshold values.
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        The genome of the mesopolyploid crop species Brassica rapa.

        We report the annotation and analysis of the draft genome sequence of Brassica rapa accession Chiifu-401-42, a Chinese cabbage. We modeled 41,174 protein coding genes in the B. rapa genome, which has undergone genome triplication. We used Arabidopsis thaliana as an outgroup for investigating the consequences of genome triplication, such as structural and functional evolution. The extent of gene loss (fractionation) among triplicated genome segments varies, with one of the three copies consistently retaining a disproportionately large fraction of the genes expected to have been present in its ancestor. Variation in the number of members of gene families present in the genome may contribute to the remarkable morphological plasticity of Brassica species. The B. rapa genome sequence provides an important resource for studying the evolution of polyploid genomes and underpins the genetic improvement of Brassica oil and vegetable crops.
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          The ABC's of comparative genomics in the Brassicaceae: building blocks of crucifer genomes.

          In this review we summarize recent advances in our understanding of phylogenetics, polyploidization and comparative genomics in the family Brassicaceae. These findings pave the way for a unified comparative genomic framework. We integrate several of these findings into a simple system of 24 conserved chromosomal blocks (labeled A-X). The naming, order, orientation and color-coding of these blocks are based on their positions in a proposed ancestral karyotype (n=8), rather than by their position in the reduced genome of Arabidopsis thaliana (n=5). We show how these crucifer building blocks can be rearranged to model the genome structures of A. thaliana, Arabidopsis lyrata, Capsella rubella and Brassica rapa. A framework for comparison between species is timely because several crucifer genome-sequencing projects are underway.
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            Author and article information

            Affiliations
            1Department of Genetics, University of Delhi South Campus , New Delhi, India
            2Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus , New Delhi, India
            Author notes

            Edited by: Maoteng Li, Huazhong University of Science and Technology, China

            Reviewed by: Leonardo Velasco, Instituto de Agricultura Sostenible (IAS), Spain; Harsh Raman, New South Wales Department of Primary Industries, Australia

            *Correspondence: Akshay K. Pradhan pradhancgmcp@ 123456gmail.com

            This article was submitted to Plant Breeding, a section of the journal Frontiers in Plant Science

            Contributors
            Journal
            Front Plant Sci
            Front Plant Sci
            Front. Plant Sci.
            Frontiers in Plant Science
            Frontiers Media S.A.
            1664-462X
            16 October 2018
            2018
            : 9
            6198181
            10.3389/fpls.2018.01448
            Copyright © 2018 Rout, Yadav, Yadava, Mukhopadhyay, Gupta, Pental and Pradhan.

            This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

            Counts
            Figures: 3, Tables: 8, Equations: 0, References: 46, Pages: 15, Words: 10222
            Funding
            Funded by: Department of Biotechnology, Ministry of Science and Technology 10.13039/501100001407
            Award ID: BT/01/COE/08/06/-II
            Award ID: BT/01/NDDB/UDSC/2016
            Categories
            Plant Science
            Original Research

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