Skim-Based Genotyping by Sequencing Using a Double Haploid Population to Call SNPs, Infer Gene Conversions, and Improve Genome Assemblies

Clubroot resistance is an economically important trait in Brassicaceae crops. Although many quantitative trait loci (QTLs) for clubroot resistance have been identified in Brassica, disease-related damage continues to occur owing to differences in host variety and constant pathogen variation. Here, we investigated the inheritance of clubroot resistance in a double haploid population developed by crossing clubroot resistant and susceptible lines “09CR500” and “09CR501”, respectively. The resistance of “09CR500” to Plasmodiophora brassicae pathotype “Banglim” was controlled as a single dominant gene, with the segregation of resistance and susceptibility being nearly 1:1. PbBrA08Banglim was identified as having a logarithm of odds value of 7.9–74.8, and a phenotypic variance of 26.0–97.1% with flanking marker “09CR.11390652” in A08. After aligning QTL regions to the B. rapa reference genome, 11 genes were selected as candidates. PbBrA08Banglim was located near Crr1, CRs, and Rcr9 loci, but differences were validated by marker analysis, gene structural variations, and gene expression levels, as well as phenotypic responses to the pathotype. Genotyping using the “09CR.11390652” marker accurately distinguished the Banglim-resistance phenotypes in the double haploid population. Thus, the developed marker will be useful in Brassica breeding programs, marker-assisted selection, and gene pyramiding to identify and develop resistant cultivars.

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Rice Anther Culture to Develop Double Haploid Population and Blast Resistant Lines

Jurnal AgroBiogen ◽

10.21082/jbio.v5n2.2009.p71-77 ◽

2009 ◽

Vol 5 (2) ◽

pp. 71

Author(s):

Dinar Ambarwati ◽

Ida H. Soemantri ◽

Dwinita W. Utami ◽

Aniversari Apriana ◽

Sugiono Moeljopawiro

Keyword(s):

Anther Culture ◽

Double Haploid ◽

Double Haploid Population ◽

Pyricularia Grisea ◽

Resistant Lines ◽

Haploid Population

Penyakit blas pada padi yang disebabkan oleh cendawan Pyricularia grisea, merupakan salah satu kendala dalam produksi beras. Sumber gen ketahanan terhadap penyakit blas dijumpai pada spesies padi liar Oryza rufipogon. Populasi silang ganda (BC2F3) turunan IR64 dan O. rufipogon mempunyai QTL untuk sifat ketahanan terhadap penyakit blas. Untuk mempercepat perolehan tanaman homosigot dari populasi tersebut, dilakukan kultur anter pada dua media induksi kalus: I1 (N6 + NAA 2 mg/l + kinetin 0,5 mg/l + sukrosa 60 g/l + putresin 0,16 g/l) dan I2 (N6 + 2,4-D 2 mg/l + sukrosa 50 g/l) dan dua media regenerasi: R1 (MS + NAA 0,5 mg/l + kinetin 2 mg/l + sukrosa 40 g/l + putresin 0,16 g/l) dan R2 (MS + NAA 1 mg/l + kinetin 2 mg/l + sukrosa 30 g/l). Kultur anter dilakukan pada sembilan genotipe, di mana tiga genotipe (149-16, 343, 337-13) memberikan respon terbaik dalam produksi planlet hijau setelah dikulturkan pada media regenerasi R1. Dari 208 planlet hasil regenerasi diperoleh 42 planlet haploid ganda dari genotipe 149-16, 11 planlet haploid ganda dari genotipe 343, dan 44 planlet haploid ganda dari genotipe 337-13. Skrining ketahanan blas di rumah kaca pada populasi haploid ganda menghasilkan 46 tanaman tahan terhadap ras 001, 33 tanaman tahan terhadap ras 033, dan 79 tanaman tahan terhadap ras 173. Sebanyak 28 tanaman bersifat tahan, baik terhadap ras 001, 033, maupun 173 seperti halnya O. rufipogon. Galur-galur homosigot ini akan diuji di lapang untuk ketahanannya terhadap penyakit blas dan karakter agronominya.

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