scholarly journals Characterization of the Common japonica-Originated Genomic Regions in the High Yielding Varieties Developed from Inter-Subspecific Crosses in Rice (Oryza sativa L.)

2020 ◽  
Author(s):  
Jeonghwan Seo ◽  
So-Myeong Lee ◽  
Jae-Hyuk Han ◽  
Na-Hyun Shin ◽  
Yoon Kyung Lee ◽  
...  
Keyword(s):  
Molecular Breeding ◽  
Snp Markers ◽  
Yield Potential ◽  
Breeding Programs ◽  
Wx Gene ◽  
High Yielding Varieties ◽  
Indica And Japonica Subspecies ◽  
Genomic Regions ◽  
Further Development

The inter-subspecific crossing between indica and japonica subspecies in rice have been utilized to improve yield potential in temperate rice. In this study, a comparative study of the genomic regions in the eight high yielding varieties (HYVs) was conducted with those of the four non-HYV varieties. NGS mapping on the Nipponbare reference genome identified a total of 14 common genomic regions of japonica-originated alleles. Interestingly, the HYVs shared the japonica-originated genomic regions on the nine chromosomes, although they were developed from different breeding programs. A panel of 94 varieties was classified into four varietal groups with the 39 SNP markers from 39 genes residing the japonica-originated genomic regions and 16 additional trait-specific SNPs. As expected, the japonica originated genomic regions were present only in JAP and HYV groups with exceptions for Chr4-1 and Chr4-2. The Wx gene located within Chr6-1 was present in HYV and JAP variety groups, while the yield-related genes were conserved as indica alleles in HYVs. The japonica-originated genomic regions and alleles shared by HYVs can be employed in molecular breeding programs for further development of HYVs in rice.

scholarly journals Characterization of the Common Japonica-Originated Genomic Regions in the High-Yielding Varieties Developed from Inter-Subspecific Crosses in Temperate Rice (Oryza sativa L.)

Genes ◽  
2020 ◽  
Vol 11 (5) ◽  
pp. 562 ◽  
Author(s):  
Jeonghwan Seo ◽  
So-Myeong Lee ◽  
Jae-Hyuk Han ◽  
Na-Hyun Shin ◽  
Yoon Kyung Lee ◽  
...  
Keyword(s):  
Oryza Sativa L ◽  
Snp Markers ◽  
Yield Potential ◽  
Breeding Programs ◽  
Wx Gene ◽  
High Yielding Varieties ◽  
Indica And Japonica Subspecies ◽  
Genomic Regions ◽  
Next Generation Sequencing Ngs

The inter-subspecific crossing between indica and japonica subspecies in rice have been utilized to improve the yield potential of temperate rice. In this study, a comparative study of the genomic regions in the eight high-yielding varieties (HYVs) was conducted with those of the four non-HYVs. The Next-Generation Sequencing (NGS) mapping on the Nipponbare reference genome identified a total of 14 common genomic regions of japonica-originated alleles. Interestingly, the HYVs shared japonica-originated genomic regions on nine chromosomes, although they were developed through different breeding programs. A panel of 94 varieties was classified into four varietal groups with 38 single nucleotide polymorphism (SNP) markers from 38 genes residing in the japonica-originated genomic regions and 16 additional trait-specific SNPs. As expected, the japonica-originated genomic regions were only present in the japonica (JAP) and HYV groups, except for Chr4-1 and Chr4-2. The Wx gene, located within Chr6-1, was present in the HYV and JAP variety groups, while the yield-related genes were conserved as indica alleles in HYVs. The japonica-originated genomic regions and alleles shared by HYVs can be employed in molecular breeding programs to further develop the HYVs in temperate rice.

scholarly journals Mapping QTL for spike fertility and related traits in two doubled haploid wheat (Triticum aestivum L.) populations

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Nicole Pretini ◽  
Leonardo S. Vanzetti ◽  
Ignacio I. Terrile ◽  
Guillermo Donaire ◽  
Fernanda G. González
Keyword(s):  
Doubled Haploid ◽  
Marker Assisted Selection ◽  
Triticum Aestivum L ◽  
Physiological Model ◽  
Yield Potential ◽  
Breeding Programs ◽  
Per Se ◽  
Genomic Regions ◽  
Fertility Traits ◽  
Selection Of

Abstract Background In breeding programs, the selection of cultivars with the highest yield potential consisted in the selection of the yield per se, which resulted in cultivars with higher grains per spike (GN) and occasionally increased grain weight (GW) (main numerical components of the yield). In this study, quantitative trait loci (QTL) for GW, GN and spike fertility traits related to GN determination were mapped using two doubled haploid (DH) populations (Baguette Premium 11 × BioINTA 2002 and Baguette 19 × BioINTA 2002). Results In total 305 QTL were identified for 14 traits, out of which 12 QTL were identified in more than three environments and explained more than 10% of the phenotypic variation in at least one environment. Eight hotspot regions were detected on chromosomes 1A, 2B, 3A, 5A, 5B, 7A and 7B in which at least two major and stable QTL sheared confidence intervals. QTL on two of these regions (R5A.1 and R5A.2) have previously been described, but the other six regions are novel. Conclusions Based on the pleiotropic analysis within a robust physiological model we conclude that two hotspot genomic regions (R5A.1 and R5A.2) together with the QGW.perg-6B are of high relevance to be used in marker assisted selection in order to improve the spike yield potential. All the QTL identified for the spike related traits are the first step to search for their candidate genes, which will allow their better manipulation in the future.

scholarly journals Mapping and Characterization QTLs for Phenological Traits in Seven Pedigree-connected Peach Families

2020 ◽  
Author(s):  
Zena Rawandoozi ◽  
Timothy Hartmann ◽  
Silvia Carpenedo ◽  
Ksenija Gasic ◽  
Cassia da Silva Linge ◽  
...  
Keyword(s):  
Prunus Persica ◽  
Phenotypic Variance ◽  
Breeding Programs ◽  
Large Tree ◽  
Early Seedling ◽  
Sib Families ◽  
Functional Alleles ◽  
Genomic Regions ◽  
Marker Identification

Abstract BackgroundEnvironmental adaptation and expanding harvest seasons are primary goals of most peach [Prunus persica (L.) Batsch] breeding programs. Breeding perennial crops is a challenging task due to their long breeding cycles and large tree size. Pedigree-based analysis using pedigreed families followed by haplotype construction creates a platform for QTL and marker identification, validation, and the use of marker-assisted selection in breeding programs.ResultsPhenotypic data of seven F1 low to medium chill full-sib families were collected over two years at two locations and genotyped using the 9K SNP Illumina array. Three QTLs were discovered for bloom date (BD) and mapped on linkage group 1 (LG1) (172 – 182 cM), LG4 (48 – 54 cM), and LG7 (62 – 70 cM), explaining 17-54%, 11-55%, and 11-18% of the phenotypic variance, respectively. The QTL for ripening date (RD) and fruit development period (FDP) on LG4 was co-localized at the central part of LG4 (40 - 46 cM) and explained between 40-75% of the phenotypic variance. Haplotype analyses revealed SNP haplotypes and predictive SNP marker(s) associated with desired QTL alleles and the presence of multiple functional alleles with different effects for a single locus for RD and FDP.ConclusionsA multiple pedigree-linked families approach validated major QTLs for the three key phenological traits which were reported in previous studies across diverse materials, geographical distributions, and QTL mapping methods. Haplotype characterization of these genomic regions differentiates this study from the previous QTL studies. Our results will provide the peach breeder with the haplotypes for three BD QTLs and one RD/FDP QTL for the creation of predictive DNA-based molecular marker tests to select parents and/or seedlings that have desired QTL alleles and cull unwanted genotypes in early seedling stages.

Molecular Characterization of Parental Lines and Validation of Snp Markers for Disease Resistance in Common Bean

2021 ◽  
Author(s):  
Lucas Matias Gomes-Messias ◽  
Rosana Pereira Vianello ◽  
Joney Pereira Monteiro-Júnior ◽  
Luana Alves Rodrigues ◽  
Ana Paula Simplício Mota ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Common Bean ◽  
Molecular Characterization ◽  
High Efficiency ◽  
Snp Markers ◽  
Molecular Tools ◽  
Breeding Programs ◽  
Efficiency Of Selection ◽  
Selection Of

Abstract The implementation of molecular tools that help the early selection of genotypes carrying target alleles increases efficiency and reduces the time and costs of breeding programs. The present study aimed the molecular characterization and validation of SNPs targeting disease resistance alleles for assisted selection. A total of 376 common bean lines with contrasting responses for anthracnose and angular leaf spot resistance were used, as well as 149 F2 plants from the cross between BRS Cometa x SEL 1308 (carrying the Anthracnose resistance gene Co-42). Seven of the ten SNP markers evaluated showed potential for assisted breeding: snpPV0025 (Phg-2), snpPV0027 (Phg-5), snpPV0079 (Phg-5), snpPV0046 (Co-u), snpPV0068 (Co-42), snpPV0070 (Co-42) and snpP8282v3-817 (Co-42). Markers snpPV0070 and snpP8282v3-817 showed high efficiency of selection (99.7 and 99.8%, respectively). These markers exhibit great potential to assist in the selection at different stages of the breeding program and may be readily incorporated into marker-assisted selection.

scholarly journals Characterization of Indonesian pigmented rice (Oryza sativa) based on morphology and Single Nucleotide Polymorphisms

2019 ◽  
Vol 20 (4) ◽  
pp. 1208-1214 ◽  
Author(s):  
NUR SITI KURNIASIH ◽  
RATNA SUSANDARINI ◽  
FEBRI ADI SUSANTO ◽  
TRI RINI NURINGTYAS ◽  
GLYN JENKINS ◽  
...  
Keyword(s):  
Oryza Sativa ◽  
Single Nucleotide Polymorphisms ◽  
Morphological Characters ◽  
Snp Markers ◽  
Hybrid Vigor ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Pigmented Rice ◽  
Indica And Japonica Subspecies

Abstract. Kurniasih NS, Susandarini R, Susanto FA, Nuringtyas TR, Jenkins G, Purwestri YA. 2019. Characterization of Indonesian pigmented rice (Oryza sativa) based on morphology and Single Nucleotide Polymorphisms. Biodiversitas 20: 1208-1214. Indonesia has many cultivars of pigmented rice, but many variants have not been characterized using morphological characters and molecular markers. SNPs (Single Nucleotide polymorphisms) have been used in previous studies to identify the Indica and Japonica subspecies. Characterization of whether a line belongs to the Indica or Japonica subspecies is useful information for rice breeders, especially to generate line exhibiting the strong hybrid vigor. Morphological characters are used to determine the relationship between cultivars using cluster analysis. The SNP markers were amplified by PCR, sequenced and compared with sequences in the GenBank. Based on morphological characters, ten cultivars divide into two clusters. SNPs distinguish Indica and Japonica subspecies, and show that Hitam Lampung, Aek Sibundong, Melik, Hitam Toraja, Merah Kalimantan, and Merah Sumbawa belong to the Indica subspecies while Cempo Ireng and Pare Eja belong to Japonica. Abang Segreng and Hitam Toraja could not be clearly assigned to either the Indica or Japonica subspecies.

scholarly journals Molecular characterization of bacterial leaf streak resistance in hard winter wheat

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7276 ◽  
Author(s):  
Sai Mukund Ramakrishnan ◽  
Jagdeep Singh Sidhu ◽  
Shaukat Ali ◽  
Navjot Kaur ◽  
Jixiang Wu ◽  
...  
Keyword(s):  
Winter Wheat ◽  
Xanthomonas Campestris ◽  
The United States ◽  
Wheat Breeding ◽  
Significant Loss ◽  
Snp Markers ◽  
Northern Great Plains ◽  
Bacterial Leaf Streak ◽  
Genomic Regions

Bacterial leaf streak (BLS) caused by Xanthomonas campestris pv. translucens is one of the major bacterial diseases threatening wheat production in the United States Northern Great Plains (NGP) region. It is a sporadic but widespread wheat disease that can cause significant loss in grain yield and quality. Identification and characterization of genomic regions in wheat that confer resistance to BLS will help track resistance genes/QTLs in future wheat breeding. In this study, we evaluated a hard winter wheat association mapping panel (HWWAMP) containing 299 hard winter wheat lines from the US hard winter wheat growing region for their reactions to BLS. We observed a range of BLS responses among the lines, importantly, we identified ten genotypes that showed a resistant reaction both in greenhouse and field evaluation. ­Genome-wide association analysis with 15,990 SNPs was conducted using an exponentially compressed mixed linear model. Five genomic regions (p < 0.001) that regulate the resistance to BLS were identified on chromosomes 1AL, 1BS, 3AL, 4AL, and 7AS. The QTLs Q.bls.sdsu-1AL, Q.bls.sdsu-1BS, Q.bls.sdsu-3AL, Q.bls.sdsu-4AL, and Q.bls.sdsu-7AS explain a total of 42% of the variation. In silico analysis of sequences in the candidate regions on chromosomes 1AL, 1BS, 3AL, 4AL, and 7AS identified 10, 25, 22, eight, and nine genes, respectively with known plant defense-related functions. Comparative analysis with rice showed two syntenic regions in rice that harbor genes for bacterial leaf streak resistance. The ten BLS resistant genotypes and SNP markers linked to the QTLs identified in our study could facilitate breeding for BLS resistance in winter wheat.

scholarly journals Mapping and characterization QTLs for phenological traits in seven pedigree-connected peach families

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Zena J. Rawandoozi ◽  
Timothy P. Hartmann ◽  
Silvia Carpenedo ◽  
Ksenija Gasic ◽  
Cassia da Silva Linge ◽  
...  
Keyword(s):  
Prunus Persica ◽  
Phenotypic Variance ◽  
Phenotypic Data ◽  
Breeding Programs ◽  
Large Tree ◽  
Early Seedling ◽  
Sib Families ◽  
Functional Alleles ◽  
Genomic Regions

Abstract Background Environmental adaptation and expanding harvest seasons are primary goals of most peach [Prunus persica (L.) Batsch] breeding programs. Breeding perennial crops is a challenging task due to their long breeding cycles and large tree size. Pedigree-based analysis using pedigreed families followed by haplotype construction creates a platform for QTL and marker identification, validation, and the use of marker-assisted selection in breeding programs. Results Phenotypic data of seven F1 low to medium chill full-sib families were collected over 2 years at two locations and genotyped using the 9 K SNP Illumina array. Three QTLs were discovered for bloom date (BD) and mapped on linkage group 1 (LG1) (172–182 cM), LG4 (48–54 cM), and LG7 (62–70 cM), explaining 17–54%, 11–55%, and 11–18% of the phenotypic variance, respectively. The QTL for ripening date (RD) and fruit development period (FDP) on LG4 was co-localized at the central part of LG4 (40–46 cM) and explained between 40 and 75% of the phenotypic variance. Haplotype analyses revealed SNP haplotypes and predictive SNP marker(s) associated with desired QTL alleles and the presence of multiple functional alleles with different effects for a single locus for RD and FDP. Conclusions A multiple pedigree-linked families approach validated major QTLs for the three key phenological traits which were reported in previous studies across diverse materials, geographical distributions, and QTL mapping methods. Haplotype characterization of these genomic regions differentiates this study from the previous QTL studies. Our results will provide the peach breeder with the haplotypes for three BD QTLs and one RD/FDP QTL to create predictive DNA-based molecular marker tests to select parents and/or seedlings that have desired QTL alleles and cull unwanted genotypes in early seedling stages.

scholarly journals Genetic diversity and population structure of ridge gourd (Luffa acutangula) accessions in a Thailand collection using SNP markers

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Grimar Abdiel Perez ◽  
Pumipat Tongyoo ◽  
Julapark Chunwongse ◽  
Hans de Jong ◽  
Anucha Wongpraneekul ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Germplasm Collection ◽  
Snp Markers ◽  
Fixation Index ◽  
Breeding Programs ◽  
Total Fixation ◽  
Unrooted Phylogenetic Tree ◽  
Luffa Acutangula ◽  
Selection Of

AbstractThis study explored a germplasm collection consisting of 112 Luffa acutangula (ridge gourd) accessions, mainly from Thailand. A total of 2834 SNPs were used to establish population structure and underlying genetic diversity while exploring the fruit characteristics together with genetic information which would help in the selection of parental lines for a breeding program. The study found that the average polymorphism information content value of 0.288 which indicates a moderate genetic diversity for this L. acutangula germplasm. STRUCTURE analysis (ΔK at K = 6) allowed us to group the accessions into six subpopulations that corresponded well with the unrooted phylogenetic tree and principal coordinate analyses. When plotted, the STRUCTURE bars to the area of collection, we observed an admixed genotype from surrounding accessions and a geneflow confirmed by the value of FST = 0.137. AMOVA based on STRUCTURE clustering showed a low 12.83% variation between subpopulations that correspond well with the negative inbreeding coefficient value (FIS =  − 0.092) and low total fixation index (FIT = 0.057). There were distinguishing fruit shapes and length characteristics in specific accessions for each subpopulation. The genetic diversity and different fruit shapes in the L. acutangula germplasm could benefit the ridge gourd breeding programs to meet the demands and needs of consumers, farmers, and vegetable exporters such as increasing the yield of fruit by the fruit width but not by the fruit length to solve the problem of fruit breakage during exportation.

scholarly journals Chromosomal Map of the Model LegumeLotus japonicus

Genetics ◽  
2002 ◽  
Vol 161 (4) ◽  
pp. 1661-1672 ◽  
Author(s):  
Andrea Pedrosa ◽  
Niels Sandal ◽  
Jens Stougaard ◽  
Dieter Schweizer ◽  
Andreas Bachmair
Keyword(s):  
Repetitive Sequences ◽  
Lotus Japonicus ◽  
Chromosome Complement ◽  
Linkage Groups ◽  
Closely Related Species ◽  
F1 Hybrid ◽  
Bac Clones ◽  
Genomic Regions ◽  
Chromosomal Map

AbstractLotus japonicus is a model plant for the legume family. To facilitate map-based cloning approaches and genome analysis, we performed an extensive characterization of the chromosome complement of the species. A detailed karyotype of L. japonicus Gifu was built and plasmid and BAC clones, corresponding to genetically mapped markers (see the accompanying article by Sandal  et al. 2002, this issue), were used for FISH to correlate genetic and chromosomal maps. Hybridization of DNA clones from 32 different genomic regions enabled the assignment of linkage groups to chromosomes, the comparison between genetic and physical distances throughout the genome, and the partial characterization of different repetitive sequences, including telomeric and centromeric repeats. Additional analysis of L. filicaulis and its F1 hybrid with L. japonicus demonstrated the occurrence of inversions between these closely related species, suggesting that these chromosome rearrangements are early events in speciation of this group.

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