@article{71e039d7322f4821bad636c2400cfd77,
title = "Construction of a versatile SNP array for pyramiding useful genes of rice",
abstract = "DNA marker-assisted selection (MAS) has become an indispensable component of breeding. Single nucleotide polymorphisms (SNP) are the most frequent polymorphism in the rice genome. However, SNP markers are not readily employed in MAS because of limitations in genotyping platforms. Here the authors report a Golden Gate SNP array that targets specific genes controlling yield-related traits and biotic stress resistance in rice. As a first step, the SNP genotypes were surveyed in 31 parental varieties using the Affymetrix Rice 44K SNP microarray. The haplotype information for 16 target genes was then converted to the Golden Gate platform with 143-plex markers. Haplotypes for the 14 useful allele are unique and can discriminate among all other varieties. The genotyping consistency between the Affymetrix microarray and the Golden Gate array was 92.8%, and the accuracy of the Golden Gate array was confirmed in 3 F2 segregating populations. The concept of the haplotype-based selection by using the constructed SNP array was proofed.",
keywords = "Gene pyramiding, MAS, QTL, Rice breeding, SNP",
author = "Yusuke Kurokawa and Tomonori Noda and Yoshiyuki Yamagata and Rosalyn Angeles-Shim and Hidehiko Sunohara and Kanako Uehara and Tomoyuki Furuta and Keisuke Nagai and Jena, {Kshirod Kumar} and Hideshi Yasui and Atsushi Yoshimura and Motoyuki Ashikari and Kazuyuki Doi",
note = "Funding Information: This work was supported in part by the SATREPS projects “Development of crop genotypes for midlands and mountain areas of north Vietnam” and “Improvement in productivity and yield stability of rice under Kenya{\textquoteright}s biotic and abiotic stress conditions through tailor-made breeding and development of cultivation methods”, and National Bio-Resource Project for Rice. The authors express their heartfelt gratitude to Professors Makoto Matsuoka, Hidemi Kitano, Mr. Nobuhiko Hanazato and JICA staffs for supporting the WISH project. The authors thank Drs. Chi-Wei Tung, Mark “Koni” Wright and Susan McCouch for their kind instruction in SNP microarray analysis. Publisher Copyright: {\textcopyright} 2015 The Authors.",
year = "2016",
month = jan,
day = "1",
doi = "10.1016/j.plantsci.2015.09.008",
language = "English",
volume = "242",
pages = "131--139",
journal = "Plant Science",
issn = "0168-9452",
publisher = "Elsevier Ireland Ltd",
}