Targeted re-sequencing and genome-wide association analysis for wood property traits in breeding population of Eucalyptus tereticornis × E. grandis

Modhumita Ghosh Dasgupta; Muneera Parveen Abdul Bari; Senthilkumar Shanmugavel; Veeramuthu Dharanishanthi; Muthusamy Muthupandi; Naveen Kumar; Shakti Singh Chauhan; Jayabharathi Kalaivanan; Haritha Mohan; Konstantin V Krutovsky; Durairaj Rajasugunasekar

doi:10.1016/j.ygeno.2021.11.013

Targeted re-sequencing and genome-wide association analysis for wood property traits in breeding population of Eucalyptus tereticornis × E. grandis

Genomics. 2021 Nov;113(6):4276-4292. doi: 10.1016/j.ygeno.2021.11.013. Epub 2021 Nov 14.

Affiliations

¹ Institute of Forest Genetics and Tree Breeding, R.S. Puram, Coimbatore 641002, India. Electronic address: ghoshm@icfre.org.
² Institute of Forest Genetics and Tree Breeding, R.S. Puram, Coimbatore 641002, India.
³ Institute of Wood Science and Technology, 18(th) Cross Malleshwaram, Bangalore 560 003, India.
⁴ Department of Forest Genetics and Forest Tree Breeding, Georg-August University of Göttingen, 37077 Göttingen, Germany; Center for Integrated Breeding Research, George-August University of Göttingen, 37075 Göttingen, Germany; Laboratory of Forest Genomics, Genome Research and Education Center, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, 660036 Krasnoyarsk, Russia; Laboratory of Population Genetics, N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991 Moscow, Russia; Department of Ecosystem Science and Management, Texas A&M University, College Station, TX 77843-2138, USA.

PMID: 34785351
DOI: 10.1016/j.ygeno.2021.11.013

Abstract

Globally, Eucalyptus plantations occupy 22 million ha area and is one of the preferred hardwood species due to their short rotation, rapid growth, adaptability and wood properties. In this study, we present results of GWAS in parents and 100 hybrids of Eucalyptus tereticornis × E. grandis using 762 genes presumably involved in wood formation. Comparative analysis between parents predicted 32,202 polymorphic SNPs with high average read depth of 269-562× per individual per nucleotide. Seventeen wood related traits were phenotyped across three diverse environments and GWAS was conducted using 13,610 SNPs. A total of 45 SNP-trait associations were predicted across two locations. Seven large effect markers were identified which explained more than 80% of phenotypic variation for fibre area. This study has provided an array of candidate genes which may govern fibre morphology in this genus and has predicted potential SNPs which can guide future breeding programs in tropical Eucalyptus.

Keywords: Candidate genes; Genetic advancement; Heritability; Hybrid progenies; Marker; Multi-environment trials; Trait association.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Eucalyptus* / genetics
Genome-Wide Association Study
Phenotype
Plant Breeding
Polymorphism, Single Nucleotide
Wood / genetics