scholarly journals Identification of Genomic Regions Controlling Leaf Scald Resistance in Sugarcane Using a Bi-parental Mapping Population and Selective Genotyping by Sequencing

2018 ◽  
Vol 9 ◽  
Author(s):  
Andres F. Gutierrez ◽  
Jeffrey W. Hoy ◽  
Collins A. Kimbeng ◽  
Niranjan Baisakh
Keyword(s):  
Mapping Population ◽  
Genotyping By Sequencing ◽  
Selective Genotyping ◽  
Leaf Scald ◽  
Genomic Regions

scholarly journals Fine-Mapping of Sorghum Stay-Green QTL on Chromosome10 Revealed Genes Associated with Delayed Senescence

Genes ◽  
2020 ◽  
Vol 11 (9) ◽  
pp. 1026 ◽  
Author(s):  
K. N. S. Usha Kiranmayee ◽  
C. Tom Hash ◽  
S. Sivasubramani ◽  
P. Ramu ◽  
Bhanu Prakash Amindala ◽  
...  
Keyword(s):  
Drought Tolerance ◽  
Fine Mapping ◽  
Mapping Population ◽  
Single Gene ◽  
Genotyping By Sequencing ◽  
Introgression Line ◽  
Genomic Region ◽  
Stay Green ◽  
Delayed Senescence ◽  
Genomic Regions

This study was conducted to dissect the genetic basis and to explore the candidate genes underlying one of the important genomic regions on an SBI-10 long arm (L), governing the complex stay-green trait contributing to post-flowering drought-tolerance in sorghum. A fine-mapping population was developed from an introgression line cross—RSG04008-6 (stay-green) × J2614-11 (moderately senescent). The fine-mapping population with 1894 F2 was genotyped with eight SSRs and a set of 152 recombinants was identified, advanced to the F4 generation, field evaluated with three replications over 2 seasons, and genotyped with the GBS approach. A high-resolution linkage map was developed for SBI-10L using 260 genotyping by sequencing—Single Nucleotide Polymorphism (GBS–SNPs). Using the best linear unpredicted means (BLUPs) of the percent green leaf area (%GL) traits and the GBS-based SNPs, we identified seven quantitative trait loci (QTL) clusters and single gene, mostly involved in drought-tolerance, for each QTL cluster, viz., AP2/ERF transcription factor family (Sobic.010G202700), NBS-LRR protein (Sobic.010G205600), ankyrin-repeat protein (Sobic.010G205800), senescence-associated protein (Sobic.010G270300), WD40 (Sobic.010G205900), CPK1 adapter protein (Sobic.010G264400), LEA2 protein (Sobic.010G259200) and an expressed protein (Sobic.010G201100). The target genomic region was thus delimited from 15 Mb to 8 genes co-localized with QTL clusters, and validated using quantitative real-time (qRT)–PCR.

scholarly journals Identification of new resistant sources against downy mildew disease from a selected set of cucumber germplasm and its wild relatives

2020 ◽  
Vol 80 (04) ◽  
Author(s):  
Jameel Akhtar ◽  
Dikshant Gautam ◽  
Ranjan Nath ◽  
A. B. Gaikwad ◽  
K. V. Bhat ◽  
...  
Keyword(s):  
Downy Mildew ◽  
Plant Disease ◽  
Mapping Population ◽  
Disease Index ◽  
Sources Of Resistance ◽  
Resistant Accession ◽  
Genomic Regions ◽  
Moderately Resistant ◽  
Agroclimatic Zones ◽  
Downy Mildew Disease

This study was undertaken to identify new sources of resistance against downy mildew of cucumber caused by Pseudoperonospora cubensis [(Berk. and Cart.) Rostow]. Pot experiments were conducted with 16 accessions each of Cucumis sativus and C. hardwickii during the years 2017 and 2018 using 12 isolates of P. cubensis representing different agroclimatic zones of India. The accession, IC331627 from Dehradun, Uttarakhand showed plant disease index (PDI) ranging from 5.55-20.35 per cent with an average PDI of 11.56 and 11.87 per cent during the years, 2017 and 2018, respectively. Hence, IC331627 was identified to be resistant against the five isolates of P. cubesis (Pc12, Pc17, Pc19, Pc21 and Pc24) and moderately resistant against one isolate (Pc22). This resistant accession C. hardwickii (IC331627) could be utilized to develop mapping population to map genomic regions conferring the resistance to downy mildew in cucumber.

scholarly journals Genetic Dissection of Grain Yield and Agronomic Traits in Maize under Optimum and Low-Nitrogen Stressed Environments

2020 ◽  
Vol 21 (2) ◽  
pp. 543 ◽  
Author(s):  
Berhanu Tadesse Ertiro ◽  
Michael Olsen ◽  
Biswanath Das ◽  
Manje Gowda ◽  
Maryke Labuschagne
Keyword(s):  
Grain Yield ◽  
Agronomic Traits ◽  
Genotyping By Sequencing ◽  
Genetic Dissection ◽  
Common Qtl ◽  
Chromosome Position ◽  
Maize Varieties ◽  
Dh Lines ◽  
Genomic Regions ◽  
Low Nitrogen

Understanding the genetic basis of maize grain yield and other traits under low-nitrogen (N) stressed environments could improve selection efficiency. In this study, five doubled haploid (DH) populations were evaluated under optimum and N-stressed conditions, during the main rainy season and off-season in Kenya and Rwanda, from 2014 to 2015. Identifying the genomic regions associated with grain yield (GY), anthesis date (AD), anthesis-silking interval (ASI), plant height (PH), ear height (EH), ear position (EPO), and leaf senescence (SEN) under optimum and N-stressed environments could facilitate the use of marker-assisted selection to develop N-use-efficient maize varieties. DH lines were genotyped with genotyping by sequencing. A total of 13, 43, 13, 25, 30, 21, and 10 QTL were identified for GY, AD ASI, PH, EH, EPO, and SEN, respectively. For GY, PH, EH, and SEN, the highest number of QTL was found under low-N environments. No common QTL between optimum and low-N stressed conditions were identified for GY and ASI. For secondary traits, there were some common QTL for optimum and low-N conditions. Most QTL conferring tolerance to N stress was on a different chromosome position under optimum conditions.

scholarly journals GWAS Discovery Of Candidate Genes for Yield-Related Traits in Peanut and Support from Earlier QTL Mapping Studies

Genes ◽  
2019 ◽  
Vol 10 (10) ◽  
pp. 803 ◽  
Author(s):  
Wang ◽  
Yan ◽  
Li ◽  
Li ◽  
Zhao ◽  
...  
Keyword(s):  
Qtl Mapping ◽  
Candidate Genes ◽  
Genome Wide Association Study ◽  
Gene Annotation ◽  
Genotyping By Sequencing ◽  
Nucleotide Polymorphisms ◽  
Market Demand ◽  
Oil Crops ◽  
A Genome ◽  
Genomic Regions

Peanut (Arachis hypogaea L.) is one of the most important oil crops worldwide, and its yet increasing market demand may be met by genetic improvement of yield related traits, which may be facilitated by a good understanding of the underlying genetic base of these traits. Here, we have carried out a genome-wide association study (GWAS) with the aim to identify genomic regions and the candidate genes within these regions that may be involved in determining the phenotypic variation at seven yield-related traits in peanut. For the GWAS analyses, 195 peanut accessions were phenotyped and/or genotyped; the latter was done using a genotyping-by-sequencing approach, which produced a total of 13,435 high-quality single nucleotide polymorphisms (SNPs). Analyses of these SNPs show that the analyzed peanut accessions can be approximately grouped into two big groups that, to some extent, agree with the botanical classification of peanut at the subspecies level. By taking this genetic structure as well as the relationships between the analyzed accessions into consideration, our GWAS analyses have identified 93 non-overlapping peak SNPs that are significantly associated with four of the studied traits. Gene annotation of the genome regions surrounding these peak SNPs have found a total of 311 unique candidate genes. Among the 93 yield-related-trait-associated SNP peaks, 12 are found to be co-localized with the quantitative trait loci (QTLs) that were identified by earlier related QTL mapping studies, and these 12 SNP peaks are only related to three traits and are almost all located on chromosomes Arahy.05 and Arahy.16. Gene annotation of these 12 co-localized SNP peaks have found 36 candidates genes, and a close examination of these candidate genes found one very interesting gene (arahy.RI9HIF), the rice homolog of which produces a protein that has been shown to improve rice yield when over-expressed. Further tests of the arahy.RI9HIF gene, as well as other candidate genes especially those within the more confident co-localized genomic regions, may hold the potential for significantly improving peanut yield.

scholarly journals Genome-wide association study (GWAS) for morphological and yield-related traits in an oil palm hybrid (Elaeis oleifera x Elaeis guineensis) population

2019 ◽  
Author(s):  
Jaime Osorio ◽  
Gina Garzón ◽  
Paola Delgadillo ◽  
Silvio Bastidas ◽  
Leidy Moreno ◽  
...  
Keyword(s):  
Association Mapping ◽  
Candidate Genes ◽  
Oil Palm ◽  
Plant Architecture ◽  
Elaeis Guineensis ◽  
Genotyping By Sequencing ◽  
Genome Wide Association ◽  
Elaeis Oleifera ◽  
Genome Wide ◽  
Genomic Regions

Abstract Background The genus Elaeis has two species of economic importance for the oil palm agroindustry: Elaeis oleifera (O), native to the Americas, and Elaeis guineensis (G), native to Africa. This work provides to our knowledge, the first association mapping study in an interspecific OxG oil palm population, which shows tolerance to pests and diseases, high oil quality, and acceptable fruit bunch production. Results Using genotyping-by-sequencing (GBS), we identified a total of 3,776 single nucleotide polymorphisms (SNPs) that were used to perform a genome-wide association analysis (GWAS) in 378 OxG hybrid population for 10 agronomic traits. Twelve genomic regions (SNPs) were located near candidate genes implicated in multiple functional categories, such as tissue growth, cellular trafficking, and physiological processes. Conclusions We provide new insights on genomic regions that mapped on candidate genes involved in plant architecture and yield. These potential candidate genes need to be confirmed for future targeted functional analyses. Associated markers to the traits of interest may be valuable resources for the development of marker-assisted selection in oil palm breeding. Keywords: Association mapping, Elaeis guineensis , Elaeis oleifera , genotyping-by-sequencing, plant architecture, yield.

scholarly journals Development of a core RFLP map in maize using an immortalized F2 population.

Genetics ◽  
1993 ◽  
Vol 134 (3) ◽  
pp. 917-930 ◽  
Author(s):  
J M Gardiner ◽  
E H Coe ◽  
S Melia-Hancock ◽  
D A Hoisington ◽  
S Chao
Keyword(s):  
Zea Mays L ◽  
Mapping Population ◽  
F2 Population ◽  
Rflp Map ◽  
Length Polymorphisms ◽  
Segregation Ratios ◽  
Maize Genetic ◽  
Immortalized F2 ◽  
Genomic Regions ◽  
Aberrant Segregation

Abstract A map derived from restriction fragment length polymorphisms (RFLPs) in maize (Zea mays L.) is presented. The map was constructed in an immortalized Tx303 x CO159 F2 mapping population that allowed for an unlimited number of markers to be mapped and pooled F3 seed to be distributed to other laboratories. A total of 215 markers consisting of 159 genomic clones, 16 isozymes and 35 cloned genes of defined function have been placed on 10 chromosomes. An examination of segregation data has revealed several genomic regions with aberrant segregation ratios favoring either parent or the heterozygote. Mapping of cloned genes and isozymes that have been previously mapped by functional criteria has provided 29 points of alignment with the classical maize genetic map. Screening of all mapped RFLP probes against a collection of U.S. Corn Belt germplasm using EcoRI, HindIII and EcoRV has resulted in a set of 97 core markers being defined. The designation of a set of core markers allows the maize genome to be subdivided into a series of bins which serve as the backbone for maize genetic information and database boundaries. The merits and applications of core markers and bins are discussed.

scholarly journals Identification of Loci Controlling the Dwarfism Trait in the White Sailfin Molly (Poecilia latipinna) Using Genome-Wide Association Studies Based on Genotyping-By-Sequencing

Genes ◽  
2019 ◽  
Vol 10 (6) ◽  
pp. 418
Author(s):  
Fan Shao ◽  
Jing Liu ◽  
Mengyuan Ren ◽  
Junying Li ◽  
Haigang Bao ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Association Studies ◽  
Genotyping By Sequencing ◽  
Genome Wide Association ◽  
Expression Level ◽  
Genome Wide Association Studies ◽  
Sailfin Molly ◽  
Genome Wide ◽  
Genomic Regions ◽  
Sailfin Mollies

Dwarfism is a condition defined by low harvest weight in fish, but also results in strange body figures which may have potential for the selective breeding of new ornamental fish strains. The objectives of this study are to reveal the physiological causes of dwarfism and identify the genetic loci controlling this trait in the white sailfin molly. Skeletons of dwarf and normal sailfin mollies were observed by X-ray radioscopy and skeletal staining. Genome-wide association studies based on genotyping-by-sequencing (n = 184) were used to map candidate genomic regions associated with the dwarfism trait. Quantitative real-time PCR was performed to determine the expression level of candidate genes in normal (n = 8) and dwarf (n = 8) sailfin mollies. We found that the dwarf sailfin molly has a short and dysplastic spine in comparison to the normal fish. Two regions, located at NW_015112742.1 and NW_015113621.1, were significantly associated with the dwarfism trait. The expression level of three candidate genes, ADAMTS like 1, Larp7 and PPP3CA, were significantly different between the dwarf and normal sailfin mollies in the hepatopancreas, with PPP3CA also showing significant differences in the vertebrae and Larp7 showing significant differences in the muscle. This study identified genomic regions and candidate genes associated with the dwarfism trait in the white sailfin molly and would provide a reference to determine dwarf-causing variations.

scholarly journals QTL-seq for the identification of candidate genes for days to flowering and leaf shape in pigeonpea

Heredity ◽  
2022 ◽  
Author(s):  
Vikas Singh ◽  
Pallavi Sinha ◽  
Jimmy Obala ◽  
Aamir W. Khan ◽  
Annapurna Chitikineni ◽  
...  
Keyword(s):  
Leaf Shape ◽  
Genotyping By Sequencing ◽  
Mapping Method ◽  
Flowering Plant ◽  
Cross Combination ◽  
Late Flowering ◽  
Days To Flowering ◽  
Genome Wide ◽  
Whole Genome Resequencing ◽  
Genomic Regions

AbstractTo identify genomic segments associated with days to flowering (DF) and leaf shape in pigeonpea, QTL-seq approach has been used in the present study. Genome-wide SNP profiling of extreme phenotypic bulks was conducted for both the traits from the segregating population (F2) derived from the cross combination- ICP 5529 × ICP 11605. A total of 126.63 million paired-end (PE) whole-genome resequencing data were generated for five samples, including one parent ICP 5529 (obcordate leaf and late-flowering plant), early and late flowering pools (EF and LF) and obcordate and lanceolate leaf shape pools (OLF and LLS). The QTL-seq identified two significant genomic regions, one on CcLG03 (1.58 Mb region spanned from 19.22 to 20.80 Mb interval) for days to flowering (LF and EF pools) and another on CcLG08 (2.19 Mb region spanned from 6.69 to 8.88 Mb interval) for OLF and LLF pools, respectively. Analysis of genomic regions associated SNPs with days to flowering and leaf shape revealed 5 genic SNPs present in the unique regions. The identified genomic regions for days to flowering were also validated with the genotyping-by-sequencing based classical QTL mapping method. A comparative analysis of the identified seven genes associated with days to flowering on 12 Fabaceae genomes, showed synteny with 9 genomes. A total of 153 genes were identified through the synteny analysis ranging from 13 to 36. This study demonstrates the usefulness of QTL-seq approach in precise identification of candidate gene(s) for days to flowering and leaf shape which can be deployed for pigeonpea improvement.

scholarly journals Molecular phylogeny and taxonomy of the Hydrangea serrata complex (Hydrangeaceae) in western Japan, including a new subspecies of H. acuminata from Yakushima

PhytoKeys ◽  
2022 ◽  
Vol 188 ◽  
pp. 49-71
Author(s):  
Shun K. Hirota ◽  
Tetsukazu Yahara ◽  
Kengo Fuse ◽  
Hiroyuki Sato ◽  
Shuichiro Tagane ◽  
...  
Keyword(s):  
Genotyping By Sequencing ◽  
Yakushima Island ◽  
Polymorphic Species ◽  
Western Japan ◽  
Previously Treated ◽  
Genomic Regions ◽  
Relationship Of ◽  
The Relationship ◽  
Its1 And Its2

According to the contemporary classification of Hydrangea native to Japan, H. serrata is a polymorphic species including six varieties. We discovered a plant identified as H. serrata, but morphologically distinct from previously known varieties, in Yakushima island where approximately 50 endemic species are known. To determine the relationship of this plant with previously known varieties, we examined morphology and constructed a highly resolved phylogeny of H. serrata and its relatives using three chloroplast genomic regions, rbcL, trnL intron, psbA-trnH, and two nuclear genomic regions, ITS1 and ITS2, and Multiplex ISSR genotyping by sequencing (MIG-seq). Based on these morphological and phylogenetic observations, we describe Hydrangea acuminata subsp. yakushimensissubsp. nov. as a newly discovered lineage in Yakushima, Japan and propose Hydrangea minamitaniistat. nov. and Hydrangea acuminata subsp. australisstat. nov. which were previously treated as varieties of H. serrata.

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