Raman, Harsh; Banks, Robert; Liu, Shengyi; Raman, Rosy; Qiu, Yu; McVittie, Brett; Rohan, Maheswaran; Li, Li; Ferdosi, Mohammad; Menz, Ian; Cowling, Wallace

Author(s)

Raman, Harsh

Banks, Robert

Liu, Shengyi

Raman, Rosy

Qiu, Yu

McVittie, Brett

Rohan, Maheswaran

Li, Li

Ferdosi, Mohammad

Menz, Ian

Cowling, Wallace

Publication Date

2018

Abstract

We propose a new paradigm for pre-breeding in canola based on genomic selection in a globally diverse pool of Brassica napus germplasm. The base population comprising over 400 diverse canola lines representing global genetic diversity in the crop was developed at NSW DPI, Wagga Wagga. In this study, we assessed genetic diversity among 368 canola lines representing Australian Brassica napus Homozygous Diversity Set (ABnHDS) by Illumina SNP markers. These lines were evaluated for early vigour, flowering time, grain yield, and resistance to blackleg under field conditions as well as for tolerance to Mn2+ under controlled environment conditions. A subset of 196 lines was also analysed for structural variations (INDELS) and SNPs using whole genome resequencing approach. Cluster and population structure analyses of ABnHDS (368 lines) grouped canola lines based on their growth habit and geographic origin. Using both molecular and phenotypic data, individual lines were assigned genomic predicted breeding values (GPBV) by genomic best linear unbiased prediction (GBLUP). Genomic prediction accuracies ranged from 47 to 80% across traits (except for 37% for flowering time under short day conditions) indicating that genomic prediction can be used quite confidently to predict the performance for some canola lines with missing phenotypes. We further employed mating design based on optimal contributions selection (OCS) to manage long-term genetic gain and genetic diversity in the global diversity pool. Canola breeders will have the accelerated access of lines with potential value in their commercial programs based on their ranking for economic index and GPBV for individual traits. The global diversity pool will also be useful to identify the role of individual genes that underlie traits of economic importance.

Citation

AusCanola 2018: 20th Australian Research Assembly on Brassicas, p. 144-150

Link

https://hdl.handle.net/1959.11/31043

Publisher

Australian Research Assembly on Brassicas

Title

Genomic selection in global diversity pools-a new paradigm for pre-breeding in canola

Type of document

Conference Publication

Entity Type

Publication

Author(s)	Raman, Harsh Banks, Robert Liu, Shengyi Raman, Rosy Qiu, Yu McVittie, Brett Rohan, Maheswaran Li, Li Ferdosi, Mohammad Menz, Ian Cowling, Wallace
Publication Date	2018
Abstract	We propose a new paradigm for pre-breeding in canola based on genomic selection in a globally diverse pool of <i>Brassica napus</i> germplasm. The base population comprising over 400 diverse canola lines representing global genetic diversity in the crop was developed at NSW DPI, Wagga Wagga. In this study, we assessed genetic diversity among 368 canola lines representing <u>A</u>ustralian <i><u>B</u>rassica <u>n</u>apus</i> <u>H</u>omozygous <u>D</u>iversity <u>S</u>et (ABnHDS) by Illumina SNP markers. These lines were evaluated for early vigour, flowering time, grain yield, and resistance to blackleg under field conditions as well as for tolerance to Mn<sup>2+</sup> under controlled environment conditions. A subset of 196 lines was also analysed for structural variations (INDELS) and SNPs using whole genome resequencing approach. Cluster and population structure analyses of ABnHDS (368 lines) grouped canola lines based on their growth habit and geographic origin. Using both molecular and phenotypic data, individual lines were assigned genomic predicted breeding values (GPBV) by genomic best linear unbiased prediction (GBLUP). Genomic prediction accuracies ranged from 47 to 80% across traits (except for 37% for flowering time under short day conditions) indicating that genomic prediction can be used quite confidently to predict the performance for some canola lines with missing phenotypes. We further employed mating design based on optimal contributions selection (OCS) to manage long-term genetic gain and genetic diversity in the global diversity pool. Canola breeders will have the accelerated access of lines with potential value in their commercial programs based on their ranking for economic index and GPBV for individual traits. The global diversity pool will also be useful to identify the role of individual genes that underlie traits of economic importance.
Citation	AusCanola 2018: 20th Australian Research Assembly on Brassicas, p. 144-150
Link	https://hdl.handle.net/1959.11/31043
Publisher	Australian Research Assembly on Brassicas
Title	Genomic selection in global diversity pools-a new paradigm for pre-breeding in canola
Type of document	Conference Publication
Entity Type	Publication

Genomic selection in global diversity pools-a new paradigm for pre-breeding in canola

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