Genome wide analysis of recurrent parent genome recovery in different backcross populations for blast resistance through SSR markers in rice

Blast Resistance Performance of Promising Lines Derived from Backcross and Double Haploid Population Between IR64 and Oryza rufipogon. Developing blast resistance varieties with superior agronomical performance has been the one of the important priorities in rice breeding program. Based on the purpose of this study the double haploid and backcross populations were developed using the most popular cultivar IR64 as recurrent parent and wild rice species Oryza rufipogon (Acc. IRGC 105491) as blast resistance donor parent. This study was initiated to analyze the blast resistance and agronomical performance of double haploid populations (DH_I, DH_II and DH_III) and backcross populations (BC2, BC3, and BC5), based on the green house and field screening tests. The results of statistical analysis showed that the blast resistance performance of DH population were diverse among DH_I, DH_II and DH_III. The smallest diversity was on the DH_III population. The same results were also detected on BC populations. The smallest diversity was on BC5 population. The diversity comparison between DH and BC population showed that DH_III population had smaller variation than BC5. Indicated that DH_III population has the most fixed population. The agronomic performance evaluation of DH_III population selected lines showed that Bio1, Bio2, and Bio8 qualitified as the candidate of promising lines. AbstrakPerakitan varietas tahan blas sebagai galur harapan, merupakan salah satu prioritas dalam program pemuliaan padi. Dalam rangka mendukung program tersebut, telah dilakukan pembentukan populasi haploid ganda (HG) dan silang balik (BC) dengan IR64 sebagai tetua berulang dan Oryza rufipogon (No. aksesi IRGC 105491) sebagai tetua donor gen tahan penyakit blas. Penelitian ini bertujuan menganalisis keragaan tingkat ketahanan galur-galur haploid ganda (HG_I, HG_II, dan HG_III) dan galur-galur silang balik (BC2, BC3, dan BC5) terhadap penyakit blas di rumah kaca dan lapang, sehingga diperoleh kandidat galur harapan. Hasil pengujian beberapa populasi HG dan BC menunjukan bahwa terdapat variasi keragaan yang berbeda-beda. Variasi paling kecil terdapat pada populasi HG_III. Hasil yang sama juga diperoleh pada populasi silang balik (BC2-BC5). Variasi paling kecil terdapat pada populasi BC5. Bila dibandingkan antar populasi HG dan BC, tingkat variasi pada populasi HG_III lebih kecil dibandingkan dengan tingkat variasi pada populasi BC5. Hal ini menunjukkan bahwa tingkat homosigositas paling tinggi terdapat pada populasi HG_III. Berdasarkan evaluasi penampilan agronomis beberapa galur HG_III terpilih, diperoleh tiga galur kandidat galur harapan Bio1, Bio2, dan Bio8.

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Molecular marker aided breeding for blast resistant rice in Nepal

Journal of Agriculture and Environment ◽

10.3126/aej.v15i0.19831 ◽

2014 ◽

Vol 15 ◽

pp. 128-138

Author(s):

Bal K Joshi ◽

Hari P Bimb ◽

Gopal Parajuli ◽

Bedanand Chaudhary

Keyword(s):

Resistance Gene ◽

Ssr Markers ◽

Bulked Segregant Analysis ◽

Blast Resistance ◽

Hot Spot ◽

Resistance Breeding ◽

Recurrent Parent ◽

Simple Method ◽

Multiple Alleles ◽

Rice Landraces

Molecular markers tightly linked to target gene have been identified in different chromosomes to impose the genetic selection. This paper summarizes the progress and achievement made in breeding for blast resistance rice based on DNA markers. At least 40 genes conferring resistance to blast isolates with multiple alleles have been described. Both dominant and recessive resistance alleles have been found in many rice landraces. Highly polymorphic and easily detectable SSR markers are being used in breeding for blast resistance. Bulked segregant analysis (BSA) is the simple method for tagging resistance gene by SSR markers. Quantitative trait loci (QTLs) have also been mapped and most of them are linked to qualitative genes. Simple sequence repeat (SSR) markers linked to the gene are being used to select plants possessing the desired trait and markers throughout the genome are being used to select plants that are genetically similar to recurrent parent. Using SSR markers it may be possible to select blast resistance genotypes at any stage of crop development from any small part of crop, to conduct many round of selection, to select without inoculums, without scoring, and without testing in hot spot or artificial inoculation. Molecular based blast resistance breeding work is necessary to initiate in Nepal focusing on resistance gene tagging in Nepalese rice landraces and utilization.

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Recovery of Recurrent Parent Genome in a Marker-Assisted Backcrossing Against Rice Blast and Blight Infections Using Functional Markers and SSRs

Plants ◽

10.3390/plants9111411 ◽

2020 ◽

Vol 9 (11) ◽

pp. 1411

Author(s):

Samuel Chibuike Chukwu ◽

Mohd Y. Rafii ◽

Shairul Izan Ramlee ◽

Siti Izera Ismail ◽

Yusuff Oladosu ◽

...

Keyword(s):

Resistance Genes ◽

Blast Resistance ◽

Leaf Blight ◽

Bacterial Leaf Blight ◽

Functional Markers ◽

Recurrent Parent ◽

Selected Lines ◽

Recurrent Parent Genome ◽

Backcross Breeding ◽

Marker Assisted Backcross Breeding

The most vital aspect of marker-assisted backcross breeding is the recurrent parent genome recovery. This enables the selection of only parents with recovered recipient/recurrent parent genome in addition to the targeted genes. The recurrent parent genome recovery (RPGR) ensures that non-desirable genomic segments are removed while the gene of interest is sustained in the recombined progenies without further segregations. This work was aimed at quantifying the RPGR of backcross populations with introgression of bacterial leaf blight resistance genes. Putra-1, a Malaysian elite variety, high yielding with inherent resistance to blast but susceptible to bacterial leaf blight (BLB), was crossed with IRBB60 which is resistant to BLB disease. The IRBB60 has four Xoo resistance genes—Xa4, xa5, xa13 and Xa21. Tightly linked polymorphic functional and SSR markers were used for foreground selection at every stage of backcrossing to select progenies with introgressed target genes. Background selection was done to quantify the percentage of RPGR in the selected lines using 79 confirmed polymorphic microsatellites. Result obtained showed that the percentage of RPGR was 80.11% at BC1F1, 95.30% at BC2F1 and 95.9% at BC2F2. The introgression of Xa4, xa5, xa13 and Xa21 Xoo resistance genes were faster through the adopted marker-assisted backcross breeding compared to what could be obtained through conventional breeding. All the 16 selected lines displayed resistance to BLB with three lines showing high resistance to the disease. The blast resistance contained in the genetic background of Putra-1 was also sustained in all the selected lines. The newly developed lines were recommended as new rice varieties for commercial cultivation.

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Genome-Wide Analysis of TaNBS Resistance Genes and Development of Chromosome 2AL-specific NBS-SSR Markers in Wheat

ACTA AGRONOMICA SINICA ◽

10.3724/sp.j.1006.2016.00795 ◽

2016 ◽

Vol 42 (6) ◽

pp. 795 ◽

Cited By ~ 1

Author(s):

Lin-Yi QIAO ◽

Jian-Zhong CHANG ◽

Hui-Juan GUO ◽

Jian-Gang GAO ◽

Jun ZHENG ◽

...

Keyword(s):

Ssr Markers ◽

Resistance Genes ◽

Genome Wide Analysis ◽

Genome Wide

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Evaluation of yellow rust resistance in backcross populations of wheat

Journal of Environmental Biology ◽

10.22438/jeb/43/1/mrn-1911 ◽

2022 ◽

Vol 43 (1) ◽

pp. 147-160

Author(s):

V. Gupta ◽

◽

M. Kumar ◽

V. Singh ◽

R.N. Sheokand ◽

...

Keyword(s):

Ssr Markers ◽

Rust Resistance ◽

Yellow Rust ◽

Recurrent Parent ◽

Single Marker Analysis ◽

Yield Attributes ◽

Promising Tool ◽

Yellow Rust Resistance ◽

Backcross Populations ◽

Pathogen Dna

Aim: To screen wheat populations derived from cross DBW17 × WH1105 for loci imparting yellow rust resistance and selection of plants using polymorphic SSRs. Methodology: The study for yellow rust resistance was carried out on two populations, i.e., BC1F2 and BC2F2. Stress was provided by planting infector rows between the blocks and by artificial inoculation using a mixture of races 46S102, 47S103 and 78S84 of stripe rust pathogen. DNA isolated from young leaves was checked for the presence of yellow rust resistance genes using gene specific primers. Results: Fifteen primers were found to be polymorphic among parents DBW17 and WH1105. Fifteen polymorphic SSR markers were dispersed over the wheat genome (AABBDD), with allele range 2-5. These polymorphic SSR markers were used to produce molecular diversity among progeny lines. Cluster analysis of parents and both the populations, showed that two parents were diverse genetically and in both backcrosses progeny lines resembled their respective recurrent parent. Single marker analysis using data revealed that primers on nine chromosomes were associated with grain yield per plant, other yield attributes and yellow rust resistance in both populations. Interpretation: This study showed that a linked marker like Xgwm582 could be a promising tool for breeding wheat with enhanced tolerance to yellow rust resistance. However, growth rates and biomass production provide reliable criteria for assessing the degree of yellow rust resistance and the ability of a plant to withstand it.

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DISCOVERY OF POTENTIAL SSR MARKERS THROUGH GENOME WIDE ANALYSIS OF MAIZE B73 GENOME

Jurnal Teknologi ◽

10.11113/jt.v77.6724 ◽

2015 ◽

Vol 77 (24) ◽

Author(s):

Rabiatul Adawiah Zainal Abidin ◽

Zulkifli Ahmad Seman ◽

Shahril Ab Razak ◽

Norzihan Abdullah ◽

Umi Kalsom Abu Bakar

Keyword(s):

Ssr Markers ◽

In Silico ◽

High Throughput Sequencing ◽

Reference Genome ◽

Dna Amplification ◽

Maize Genome ◽

Dinucleotide Repeats ◽

Sequencing Platform ◽

Genome Wide Analysis ◽

Genome Wide

In silico analysis provides an economical approach in the development of simple sequence repeat (SSR) markers through utilization of genome sequences generated from high throughput sequencing platform. In this study, we present the potential SSR markers of maize mining from its reference genome of cultivar B73. In total, 94, 534 putative SSRs were detected in maize reference genome B73. Dinucleotide repeats (57.00%) were found the most frequent repeats in maize genome, followed by trinucleotide (38.90%), tetranucleotide (2.77%), pentanucleotide (0.85%) and hexanucleotide (0.48%) repeats. A total of 2239 primer pairs were successfully designed for experimental validation. Of these, 99 SSR markers were selected for optimization and only 71(71.71%) SSR primer pairs produced DNA amplification products and therefore validated as developed SSR markers for maize. This in silico approach through genome wide analysis of maize genome not only provides rapid discovery and cost effective methods in SSR markers development but also will act as useful tool for genetic diversity and marker-trait association in maize.

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