Ultra-high-throughput DArTseq-based silicoDArT and SNP markers for genomic studies in macadamia

PloS One
Mobashwer AlamBruce Topp

Abstract

Macadamia (Macadamia integrifolia, M. tetraphylla and hybrids) is an Australian native nut crop and has a significant economic value in the food industries worldwide. Long juvenility along with traditional breeding strategies impede quick genetic improvement of this crop. The existing cultivars constitute only second to fourth generation of the wild germplasm in the rainforest. The utilisation of molecular markers for genomic selection and genome-wide association studies may accelerate genetic gains. Identification of a robust, reproducible, and cost-effective marker system is instrumental in increasing the efficiency of genomic studies. This study is the first to report the potential of two ultra-high-throughput diversity array technology (DArT) markers (silicoDArT and SNP) in macadamia. Both markers were used to identify the genetic diversity and population structure in 80 macadamia cultivars. Parentage analysis of 25 scions in a rootstock trial was conducted to confirm plant identity where recorded identities did not corroborate with phenotypic field observations. A total of 22,280 silicoDArT and 7,332 SNP markers were reported, of which 11,526 silicoDArT and 3,956 SNP markers were used for analyses after screening with qual...Continue Reading

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Citations

Dec 24, 2018·Molecular Ecology·Sarah P Flanagan, Adam G Jones
Aug 14, 2020·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Jared CrainJesse Poland
Sep 26, 2021·Journal of Applied Genetics·Mateusz DydaMaria Wędzony
Nov 9, 2021·Frontiers in Plant Science·Felipe Bitencourt MartinsAnete Pereira de Souza

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Methods Mentioned

BETA
genotyping
electrophoresis
dissection

Software Mentioned

STRUCTURE
Cervus
DarTsoft14
DArT
DArTdb
silicoDArT
GenAlEx
silicoDArTs

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