Tagging and mapping of a rice gall midge resistance gene, Gm8, and development of SCARs for use in marker-aided selection and gene pyramiding

Abstract

Using amplified fragment length polymorphisms (AFLPs) and random amplified polymorphic DNAs (RAPDs), we have tagged and mapped Gm8, a gene conferring resistance to the rice gall midge (Orseolia oryzae), a major insect pest of rice, onto rice chromosome 8. Using AFLPs, two fragments, AR257 and AS168, were identified that were linked to the resistant and susceptible phenotypes, respectively. Another resistant phenotype-specific marker, AP19(587), was also identified using RAPDs. SCAR primers based on the sequence of the fragments AR257 and AS168 failed to reveal polymorphism between the resistant and the susceptible parents. However, PCR using primers based on the regions flanking AR257 revealed polymorphism that was phenotype-specific. In contrast, PCR carried out using primers flanking the susceptible phenotype-associated fragment AS168 produced a monomorphic fragment. Restriction digestion of these monomorphic fragments revealed polymorphism between the susceptible and resistant parents. Nucleotide BLAST searches revealed that the three fragments show strong homology to rice PAC and BAC clones that formed a contig representing the short arm of chromosome 8. PCR amplification using the above-mentioned primers on a larger population, derived from a cross between two indica rice varieties, Jhitpiti (resistant parent) and TN1 (susceptible parent), showed that there is a tight linkage between the markers and the Gm8 locus. These markers, therefore, have potential for use in marker-aided selection and pyramiding of Gm8 along with other previously tagged gall midge resistance genes [ Gm2, Gm4(t), and Gm7].

Identifikasi dan Aplikasi Marka Berbasis PCR untuk Identifikasi Varietas Padi dengan Palatabilitas Tinggi

“…Karena pita DNA selain target amplikon lain di RAPD juga muncul, maka modifikasi menjadi marka STS atau SCAR yang dikembangkan berdasarkan RAPD lebih dianjurkan. Marka STS berhasil dikembangkan dari AFLP dan RAPD untuk mengidentifikasi lokasi kromosom untuk gen ketahanan patogen pada padi (Jain et al, 2004). Primer STS hasil pengembangan dari RAPD yang telah digunakan untuk mengidentifikasi varietas padi premium Jepang, Koshihikari (Ohtsubo et al, 2002) dan galur isogeniknya (Nakamura et al, 2004), digunakan dalam penelitian ini dan diobservasi pada varietas padi japonica dan indica.…”

“…Marka STS atau SCAR yang dikembangkan dari RAPD (Jain et al, 2004) dianggap lebih reproducible dan mudah aplikasinya (Stewart dan Via, 1993). Marka STS hasil pengembangan dari RAPD berhasil mendiferensiasi padi japonica berdasarkan palatabilitas dan beras ketan (Ohtsubo et al, 2001).…”

Flanking Microsatellite Markers for Breeding Varieties Against Asian Rice Gall Midge

“…AFLP derived SCAR markers, SA598 on chromosome4 was found to be linked to the gall midge resistance gene, Gm7 in the rice cv. RP2333-156-8 (Sardesai et al 2002Jain et al 2004) identified an AFLP marker, AR257 and RAPD marker, AP19 587 on chromosome8 linked to the gall midge resistance gene, Gm8 in the rice cv. Jhitipiti.…”

Flanking SSR markers for allelism test for the Asian rice gall midge (Orseolia oryzae) resistance genes

“…Eight of the ten gall midge resistant genes have been tagged using various molecular markers (Nair et al 1995;Mohan et al 1997;Katiyar et al 2000Katiyar et al , 2001Sardesai et al 2002;Biradar et al 2004;Jain et al 2004). Since some of these markers were not useful in other breeding populations, additional closely linked SSR markers were identified .…”