• Title, Summary, Keyword: recurrent parent genome

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Recurrent parent genome (RPG) recovery analysis in a marker-assisted backcross breeding based on the genotyping-by-sequencing in tomato (Solanum lycopersicum L.) (토마토 MABC 육종에서 GBS(genotyping-by-sequencing)에 의한 RPG(recurrent parent genome) 회복률 분석)

  • Kim, Jong Hee;Jung, Yu Jin;Seo, Hoon Kyo;Kim, Myong-Kwon;Nou, Ill-Sup;Kang, Kwon Kyoo
    • Journal of Plant Biotechnology
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    • v.46 no.3
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    • pp.165-171
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    • 2019
  • Marker-assisted backcrossing (MABC) is useful for selecting an offspring with a highly recovered genetic background for a recurrent parent at early generation to various crops. Moreover, marker-assisted backcrossing (MABC) along with marker-assisted selection (MAS) contributes immensely to overcome the main limitation of the conventional breeding and it accelerates recurrent parent genome (RPG) recovery. In this study, we were employed to incorporate rin gene(s) from the donor parent T13-1084, into the genetic background of HK13-1151, a popular high-yielding tomato elite inbred line that is a pink color fruit, in order to develop a rin HK13-1084 improved line. The recurrent parent genome recovery was analyzed in early generations of backcrossing using SNP markers obtained from genotyping-by-sequencing analysis. From the $BC_1F_1$ and $BC_2F_1$ plants, 3,086 and 4868 polymorphic SNP markers were obtained via GBS analysis, respectively. These markers were present in all twelve chromosomes. The background analysis revealed that the extent of RPG recovery ranged from 56.7% to 84.5% and from 87.8% to 97.8% in $BC_1F_1$ and $BC_2F_1$ generations, respectively. In this study, No 5-1 with 97.8% RPG recovery rate among $BC_2F_1$ plants was similar to HK13-1151 strain in the fruit shape. Therefore, the selected plants were fixed in $BC_2F_2$ generation through selfing. MAS allowed identification of the plants that are more similar to the recurrent parent for the loci evaluated in the backcross generations. MABC can greatly reduce breeding time as compared to the conventional backcross breeding. For instance, MABC approach greatly shortened breeding time in tomato.

Marker-Assisted Foreground and Background Selection of Near Isogenic Lines for Bacterial Leaf Pustule Resistant Gene in Soybean

  • Kim, Kil-Hyun;Kim, Moon-Young;Van, Kyu-Jung;Moon, Jung-Kyung;Kim, Dong-Hyun;Lee, Suk-Ha
    • Journal of Crop Science and Biotechnology
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    • v.11 no.4
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    • pp.263-268
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    • 2008
  • Bacterial leaf pustule (BLP) caused by Xanthomonas axonopodis pv. glycines is a serious disease to make pustule and chlorotic haloes in soybean [Glycine max (L). Merr.]. While inheritance mode and map positions of the BLP resistance gene, rxp are known, no sequence information of the gene was reported. In this study, we made five near isogenic lines (NILs) from separate backcrosses (BCs) of BLP-susceptible Hwangkeumkong $\times$ BLP-resistant SS2-2 (HS) and BLP-susceptible Taekwangkong$\times$ SS2-2 (TS) through foreground and background selection based on the four-stage selection strategy. First, 15 BC individuals were selected through foreground selection using the simple sequence repeat (SSR) markers Satt486 and Satt372 flanking the rxp gene. Among them, 11 BC plants showed the BLP-resistant response. The HS and TS lines chosen in foreground selection were again screened by background selection using 118 and 90 SSR markers across all chromosomes, respectively. Eventually, five individuals showing greater than 90% recurrent parent genome content were selected in both HS and TS lines. These NILs will be a unique biological material to characterize the rxp gene.

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The Construction of a Chinese Cabbage Marker-assisted Backcrossing System Using High-throughput Genotyping Technology

  • Kim, Jinhee;Kim, Do-Sun;Lee, Eun Su;Ahn, Yul-Kyun;Chae, Won Byoung;Lee, Soo-Seong
    • Horticultural Science & Technology
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    • v.35 no.2
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    • pp.232-242
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    • 2017
  • The goal of marker-assisted backcrossing (MAB) is to significantly reduce the number of breeding generations required by using genome-based molecular markers to select for a particular trait; however, MAB systems have only been developed for a few vegetable crops to date. Among the types of molecular markers, SNPs (single-nucleotide polymorphisms) are primarily used in the analysis of genetic diversity due to their abundance throughout most genomes. To develop a MAB system in Chinese cabbage, a high-throughput (HT) marker system was used, based on a previously developed set of 468 SNP probes (BraMAB1, Brassica Marker Assisted Backcrossing SNP 1). We selected a broad-spectrum TuMV (Turnip mosaic virus) resistance (trs) Chinese cabbage line (SB22) as a donor plant, constructing a $BC_1F_1$ population by crossing it with the TuMV-susceptible 12mo-682-1 elite line. Foreground selection was performed using the previously developed trsSCAR marker. Background selection was performed using 119 SNP markers that showed clear polymorphism between donor and recipient plants. The background genome recovery rate (% recurrent parent genome recovery; RPG) was good, with three of 75 $BC_1F_1$ plants showing a high RPG rate of over 80%. The background genotyping result and the phenotypic similarity between the recurrent parent and $BC_1F_1$ showed a correlation. The plant with the highest RPG recovery rate was backcrossed to construct the $BC_2F_1$ population. Foreground selection and background selection were performed using 169 $BC_2F_1$ plants. This study shows that, using MAB, we can recover over 90% of the background genome in only two generations, highlighting the MAB system using HT markers as a highly efficient Brassica rapa backcross breeding system. This is the first report of the application of a SNP marker set to the background selection of Chinese cabbage using HT SNP genotyping technology.

Evaluation of Germplasm and Development of SSR Markers for Marker-assisted Backcross in Tomato (분자마커 이용 여교잡 육종을 위한 토마토 유전자원 평가 및 SSR 마커 개발)

  • Hwang, Ji-Hyun;Kim, Hyuk-Jun;Chae, Young;Choi, Hak-Soon;Kim, Myung-Kwon;Park, Young-Hoon
    • Horticultural Science & Technology
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    • v.30 no.5
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    • pp.557-567
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    • 2012
  • This study was conducted to achieve basal information for the development of tomato cultivars with disease resistances through marker-assisted backcross (MAB). Ten inbred lines with TYLCV, late blight, bacterial wilt, or powdery mildew resistance and four adapted inbred lines with superior horticultural traits were collected, which can be useful as the donor parents and recurrent parents in MAB, respectively. Inbred lines collected were evaluated by molecular markers and bioassay for confirming their disease resistances. To develop DNA markers for selecting recurrent parent genome (background selection) in MAB, a total of 108 simple sequence repeat (SSR) primer sets (nine per chromosome at average) were selected from the tomato reference genetic maps posted on SOL Genomics Network. Genetic similarity and relationships among the inbred lines were assessed using a total of 303 polymorphic SSR markers. Similarity coefficient ranged from 0.33 to 0.80; the highest similarity coefficient (0.80) was found between bacterial wilt-resistant donor lines '10BA333' and '10BA424', and the lowest (0.33) between a late blight resistant-wild species L3708 (S. pimpinelliforium L.) and '10BA424'. UPGMA analysis grouped the inbred lines into three clusters based on the similarity coefficient 0.58. Most of the donor lines of the same resistance were closely related, indicating the possibility that these lines were developed using a common resistance source. Parent combinations (donor parent ${\times}$ recurrent parent) showing appropriate levels of genetic distance and SSR marker polymorphism for MAB were selected based on the dendrogram. These combinations included 'TYR1' ${\times}$ 'RPL1' for TYLCV, '10BA333' or '10BA424' ${\times}$ 'RPL2' for bacterial wilt, and 'KNU12' ${\times}$ 'AV107-4' or 'RPL2' for powdery mildew. For late blight, the wild species resistant line 'L3708' was distantly related to all recurrent parental lines, and a suitable parent combination for MAB was 'L3708' ${\times}$ 'AV107-4', which showed a similarity coefficient of 0.41 and 45 polymorphic SSR markers.

Marker Assisted Development and Characterization of Beta-Carotene Rice

  • Yang, Paul;Song, Mi-Hee;Ha, Sun-Hwa;Kim, Jae-Kwang;Park, Jong-Seok;Ahn, Sang-Nag
    • Korean Journal of Breeding Science
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    • v.43 no.5
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    • pp.360-367
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    • 2011
  • Beta-carotene producing transformants were produced in the background of 'Nagdongbyeo', a Japonica rice cultivar. Introgression of the carotenoid locus in the transformant, PAC4-2 into the elite cultivar 'Ilpumbyeo' was started. To initiate a backcrossing program, we surveyed 220 SSR markers and found that 38% of them were polymorphic between 'Ilpumbyeo' as a recurrent parent and the PAC4-2 as a recipient parent. The selection strategy comprising foreground and background selection was employed. First, foreground selection was practiced in $BC_1$, $BC_2$, and $BC_3$ generations using the transgene specific PCR-based marker in addition to visual scoring of the seed color. Marker-based background selection combined with phenotypic selection was employed from $BC_3F_2$ to $BC_3F_4$ generations. Blast search indicated that the transgene PAC4-2 was located between SSR markers, RM6 and RM482. 240 $BC_3F_3$ and 63 $BC_3F_4$ lines were evaluated for four agronomic traits including days to heading. Most of the lines were similar to Ilpumbyeo in agronomic traits evaluated. The percentage of PAC4-2 genome ranged from 4% to 21% with a mean of 12.5%, which was higher than the expected for an unselected $BC_3$ backcross population. This could be explained by the fact that two genes for beta-carotene and the stripe virus resistance were targeted in this study. We selected 10 representative $BC_3F_5$ lines from 63 $BC_3F_4$ lines based on agronomic traits and carotenoids content. The selection strategy would be appropriate for the introgression of beta-carotene gene in a breeding program.

Development of SNP marker set for marker-assisted backcrossing (MABC) in cultivating tomato varieties

  • Park, GiRim;Jang, Hyun A;Jo, Sung-Hwan;Park, Younghoon;Oh, Sang-Keun;Nam, Moon
    • Korean Journal of Agricultural Science
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    • v.45 no.3
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    • pp.385-400
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    • 2018
  • Marker-assisted backcrossing (MABC) is useful for selecting offspring with a highly recovered genetic background for a recurrent parent at early generation unlike rice and other field crops. Molecular marker sets applicable to practical MABC are scarce in vegetable crops including tomatoes. In this study, we used the National Center for Biotechnology Information- short read archive (NCBI-SRA) database that provided the whole genome sequences of 234 tomato accessions and selected 27,680 tag-single nucleotide polymorphisms (tag-SNPs) that can identify haplotypes in the tomato genome. From this SNP dataset, a total of 143 tag-SNPs that have a high polymorphism information content (PIC) value (> 0.3) and are physically evenly distributed on each chromosome were selected as a MABC marker set. This marker set was tested for its polymorphism in each pairwise cross combination constructed with 124 of the 234 tomato accessions, and a relatively high number of SNP markers polymorphic for the cross combination was observed. The reliability of the MABC SNP set was assessed by converting 18 SNPs into Luna probe-based high-resolution melting (HRM) markers and genotyping nine tomato accessions. The results show that the SNP information and HRM marker genotype matched in 98.6% of the experiment data points, indicating that our sequence analysis pipeline for SNP mining worked successfully. The tag-SNP set for the MABC developed in this study can be useful for not only a practical backcrossing program but also for cultivar identification and F1 seed purity test in tomatoes.

Single Nucleotide Polymorphism Marker Discovery from Transcriptome Sequencing for Marker-assisted Backcrossing in Capsicum

  • Kang, Jin-Ho;Yang, Hee-Bum;Jeong, Hyeon-Seok;Choe, Phillip;Kwon, Jin-Kyung;Kang, Byoung-Cheorl
    • Horticultural Science & Technology
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    • v.32 no.4
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    • pp.535-543
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    • 2014
  • Backcross breeding is the method most commonly used to introgress new traits into elite lines. Conventional backcross breeding requires at least 4-5 generations to recover the genomic background of the recurrent parent. Marker-assisted backcrossing (MABC) represents a new breeding approach that can substantially reduce breeding time and cost. For successful MABC, highly polymorphic markers with known positions in each chromosome are essential. Single nucleotide polymorphism (SNP) markers have many advantages over other marker systems for MABC due to their high abundance and amenability to genotyping automation. To facilitate MABC in hot pepper (Capsicum annuum), we utilized expressed sequence tags (ESTs) to develop SNP markers in this study. For SNP identification, we used Bukang $F_1$-hybrid pepper ESTs to prepare a reference sequence through de novo assembly. We performed large-scale transcriptome sequencing of eight accessions using the Illumina Genome Analyzer (IGA) IIx platform by Solexa, which generated small sequence fragments of about 90-100 bp. By aligning each contig to the reference sequence, 58,151 SNPs were identified. After filtering for polymorphism, segregation ratio, and lack of proximity to other SNPS or exon/intron boundaries, a total of 1,910 putative SNPs were chosen and positioned to a pepper linkage map. We further selected 412 SNPs evenly distributed on each chromosome and primers were designed for high throughput SNP assays and tested using a genetic diversity panel of 27 Capsicum accessions. The SNP markers clearly distinguished each accession. These results suggest that the SNP marker set developed in this study will be valuable for MABC, genetic mapping, and comparative genome analysis.