e-journal

A whole-genome SNP array (RICE6K) for genomic breeding in rice

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The advances in genotyping technology provide an opportunity to use genomic tools in crop
breeding. As compared to field selections performed in conventional breeding programmes,
genomics-based genotype screen can potentially reduce number of breeding cycles and more
precisely integrate target genes for particular traits into an ideal genetic background. We
developed a whole-genome single nucleotide polymorphism (SNP) array, RICE6K, based on
Infinium technology, using representative SNPs selected from more than four million SNPs
identified from resequencing data of more than 500 rice landraces. RICE6K contains 5102 SNP
and insertion–deletion (InDel) markers, about 4500 of which were of high quality in the tested
rice lines producing highly repeatable results. Forty-five functional markers that are located inside
28 characterized genes of important traits can be detected using RICE6K. The SNP markers are
evenly distributed on the 12 chromosomes of rice with the average density of 12 SNPs per 1 Mb
and can provide information for polymorphisms between indica and japonica subspecies as well
as varieties within indica and japonica groups. Application tests of RICE6K showed that the array
is suitable for rice germplasm fingerprinting, genotyping bulked segregating pools, seed
authenticity check and genetic background selection. These results suggest that RICE6K provides
an efficient and reliable genotyping tool for rice genomic breeding.

Keywords: RICE6K, SNP chip,genomic breeding, functional markers,rice (Oryza sativa L.).

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Informasi Detail

Judul Seri

Plant Biotechnology Journal

No. Panggil

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Penerbit

: Society for Experimental Biology, Association of Applied Biologists and John Wiley & Sons Ltd., 2014

Deskripsi Fisik

Plant Biotechnology Journal (2014) 12, pp. 28–37

Bahasa

English

ISBN/ISSN

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Klasifikasi

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Tipe Isi

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Tipe Media

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Tipe Pembawa

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Edisi

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Subjek

PERTANIAN.

Info Detail Spesifik

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Pernyataan Tanggungjawab

Agus

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