Genetic mapping and a new PCR-based marker linked to a dwarfing gene in oat (Avena sativa L.)

Genome ◽  
2018 ◽  
Vol 61 (7) ◽  
pp. 497-503
Author(s):  
Jun Zhao ◽  
Xueqin Tang ◽  
Charlene P. Wight ◽  
Nicholas A. Tinker ◽  
Yunfeng Jiang ◽  
...  
Keyword(s):  
Avena Sativa ◽  
Positional Cloning ◽  
Ssr Marker ◽  
Bulked Segregant Analysis ◽  
Snp Markers ◽  
Consensus Map ◽  
Mapping Data ◽  
Dwarfing Gene ◽  
Production Environments ◽  
Simple Sequence

Short straw is a desired trait in cultivated hexaploid oat (Avena sativa L.) for some production environments. Marker-assisted selection, a key tool for achieving this objective, is limited by a lack of mapping data and available markers. Here, bulked-segregant analysis was used to identify PCR-based markers associated with a dwarfing gene. Genetic analysis identified a monogenic dominant inheritance of one dwarfing gene from WAOAT2132, temporarily designated DwWA. A simple sequence repeat (SSR) marker (AME117) that was already available and a new codominant PCR-based marker (bi17) developed by homologous cloning in the present study were both associated with the dwarfing gene. The two markers were located 21 and 1.2 cM from DwWA, respectively. The bi17 marker was mapped to neighboring SNP markers on chromosome 18D of the oat consensus map. Since Dw6 was previously mapped on chromosome 18, and since our new marker bi17 is also diagnostic for NILs generated for Dw6, there is strong evidence that the dwarfing gene identified in WAOAT2132 is Dw6. The newly developed markers could find applications in the identification of this gene in oat germplasm and in the fine mapping or positional cloning of the gene.

Generation of SNP markers for short straw in oat (Avena sativa L.)

Genome ◽  
2006 ◽  
Vol 49 (3) ◽  
pp. 282-287 ◽  
Author(s):  
Pirjo Tanhuanpää ◽  
Ruslan Kalendar ◽  
Jaana Laurila ◽  
Alan H Schulman ◽  
Outi Manninen ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Avena Sativa ◽  
Marker Assisted Selection ◽  
Rapd Markers ◽  
Bulked Segregant Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Snp Markers ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Dwarfing Gene

Short straw is a desired trait in oat germplasm (Avena sativa L.). Marker-assisted selection, a key tool for achieving this objective, is limited by the presence and number of available markers. Here, we have attempted to develop markers sufficiently linked to a gene specifying short straw so that marker-assisted selection could be applied. Bulked-segregant analysis was used to identify anonymous PCR-based markers associated with the dwarfing gene Dw6 in an F2 population from the cross between A. sativa 'Aslak' and A. sativa 'Kontant'. One random amplified polymorphic DNA (RAPD) and 1 retrotransposon-microsatellite amplified polymorphism (REMAP) marker were found to be associated with height. These were converted into codominant single-nucleotide polymorphism (SNP) markers. The SNP–REMAP and the SNP–RAPD markers were located 5.2 and 12.6 cM from Dw6, respectively. They can be used in future efforts both to enhance oat germplasm by application of molecular markers and to determine the nature of the gene through positional cloning.Key words: Avena sativa, short straw, marker-assisted selection, RAPD, REMAP, SNP.

Genetic map of lps3: a new short petiole gene in soybeans

Genome ◽  
2012 ◽  
Vol 55 (2) ◽  
pp. 140-146 ◽  
Author(s):  
Tae-Hwan Jun ◽  
Sung-Taeg Kang
Keyword(s):  
Ssr Marker ◽  
Bulked Segregant Analysis ◽  
Recessive Gene ◽  
Genomic Region ◽  
Snp Markers ◽  
High Yield ◽  
Plant Canopy ◽  
Single Recessive Gene ◽  
Genomic Location ◽  
Soybean Plants

The short petiole trait is valuable for the development of plant ideotypes with high yield by improving the plant canopy. The soybean breeding line SS98206SP has shown extremely short petioles in the greenhouse and fields. A new single recessive gene designated as lps3 confers the short petiole trait in SS98206SP. The objectives of this study were to map the short petiole gene in SS98206SP with PCR-based markers. In total, 187 F2 plants and their F2:3 families from a cross between the short petiole line SS98206SP and the long petiole cultivar ‘Taekwang’ along with the two parental lines were evaluated for their petiole lengths in a greenhouse. An SSR marker from each 10-cM section of a consensus soybean map was selected for bulked segregant analysis (BSA) to identify the tentative genomic location of the gene. The BSA technique was useful to localize the gene to a genomic region in the soybean linkage group F (chromosome 13). A linkage map with six SSR and two SNP markers flanking the gene was constructed. We positioned the gene between two SSR markers, Sat_234 and Sct_033, at distances of 8.5 and 3.5 cM from the marker, respectively. The makers flanking the gene (lps3) were located within 3–4 cM of the gene. These markers will be useful for maker-assisted selection in the development of new ideotype soybean plants.

scholarly journals Brassica napus L. dwarfing gene: Determining candidate intervals of dwarfing genes by BSA and SNP typing

2020 ◽  
Author(s):  
Luo Jing ◽  
Li Chao ◽  
Zhang Ruimao ◽  
Chen Zhineng ◽  
Zhang Xianqiang ◽  
...  
Keyword(s):  
Plant Height ◽  
Bulked Segregant Analysis ◽  
Snp Markers ◽  
The Other ◽  
Dwarfing Genes ◽  
Brassica Napus L ◽  
Dwarfing Gene ◽  
The One ◽  
Polymorphism Screening ◽  
Candidate Interval

AbstractThe plant height of rapeseed is one of the important factors that affects the production of rapeseed. If the plant height of rapeseed is too high, on the one hand, it will cause rapeseed to lodge and affect the yield, on the other hand, it will also affect the mechanized harvesting of rapeseed. In this research, the high-stalked line (YY50) and the dwarfed line (DW871) are crossed to obtain an F2 rapeseed population which was used to build pools, and then we used this to mine the main dwarfing genes. In the pools composed of tall and short stalks, we obtained 192.80Mb clean reads, which can be used for BSA (bulked segregant analysis). Preliminary positioning around the candidate section identified 23 SNP markers. Then 17 polymorphic SNP markers were obtained through polymorphism screening. Further we narrowed the candidate interval, and finally determined between 15.51-16.60Mb of ChrA10. Through identifying 231 genes from the above interval, it’s predicted that the production of dwarf traits may be related to lignin synthesis and limited inflorescence. It provides a basis for further mapping and cloning of the dwarfing gene DW871.

scholarly journals Position Validation of the Dwarfing Gene Dw6 in Oat (Avena sativa L.) and Its Correlated Effects on Agronomic Traits

2021 ◽  
Vol 12 ◽  
Author(s):  
Honghai Yan ◽  
Kaiquan Yu ◽  
Yinghong Xu ◽  
Pingping Zhou ◽  
Jun Zhao ◽  
...  
Keyword(s):  
Plant Height ◽  
Avena Sativa ◽  
Positional Cloning ◽  
Agronomic Traits ◽  
Single Gene ◽  
Kernel Weight ◽  
Potential Yield ◽  
Coleoptile Length ◽  
Dwarfing Gene ◽  
Kernel Length

An F6:8 recombinant inbred line (RIL) population derived from the cross between WAOAT2132 (Dw6) and Caracas along with the two parents were used to evaluate the genetic effects of Dw6 dwarfing gene on plant height and other agronomic traits in oat (Avena sativa L.) across three environments, and develop closely linked markers for marker-assisted selection (MAS) for Dw6. The two parents differed in all investigated agronomic traits except for the number of whorls. The RIL lines showed a bimodal distribution for plant height in all three tested environments, supporting the height of this population was controlled by a single gene. Dw6 significantly reduced plant height (37.66∼44.29%) and panicle length (13.99∼22.10%) but without compromising the coleoptile length which was often positively associated with the reduced stature caused by dwarfing genes. Dw6 has also strong negative effects on hundred kernel weight (14.00∼29.55%), and kernel length (4.21∼9.47%), whereas the effects of Dw6 on the kernel width were not uniform across three environments. By contrast, lines with Dw6 produced more productive tillers (10.11∼10.53%) than lines without Dw6. All these together suggested the potential yield penalty associated with Dw6 might be partially due to the decrease of kernel weight which is attributed largely to the reduction of kernel length. Eighty-one simple sequence repeat (SSR) primer pairs from chromosome 6D were tested, five of them were polymorphic in two parents and in two contrasting bulks, confirming the 6D location of Dw6. By using the five polymorphic markers, Dw6 was mapped to an interval of 1.0 cM flanked by markers SSR83 and SSR120. Caution should be applied in using this information since maker order conflicts were observed. The close linkages of these two markers to Dw6 were further validated in a range of oat lines. The newly developed markers will provide a solid basis for future efforts both in the identification of Dw6 in oat germplasm and in the determination of the nature of the gene through positional cloning.

scholarly journals Consensus Genetic Linkage Map Construction Based on One Common Parental Line for QTL Mapping in Wheat

Agronomy ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 227
Author(s):  
Xin Hu ◽  
Yingquan Zhang ◽  
Jingjuan Zhang ◽  
Shahidul Islam ◽  
Maoyun She ◽  
...  
Keyword(s):  
Qtl Mapping ◽  
Positional Cloning ◽  
Coat Color ◽  
Physical Map ◽  
Wheat Breeding ◽  
Snp Markers ◽  
Genetic Maps ◽  
Parental Line ◽  
Seed Color ◽  
Consensus Map

The consensus map is used for the verification of marker order, quantitative trait locus (QTL) mapping and molecular marker-assisted selection (MAS) in wheat breeding. In this study, a wheat consensus genetic map named as Sp7A_G7A, was constructed using 5643 SNP markers in two double haploid (DH) populations of Spitfire × Bethlehem-7AS (Sp7A) and Gregory × Bethlehem-7AS (G7A), covering 4376.70 cM of 21 chromosomes (chr) with an average interval of 0.78 cM. The collinearity of the linkage maps with the consensus map of Con_map_Wang2014 and the physical map of wheat reference genome (IWGSC RefSeq v1.0) were analyzed based on the Spearman rank correlation coefficients. As results, the three constructed genetic maps of Sp7A, G7A and Sp7A_G7A showed high collinearity with the Con_map_Wang2014 and the physical map, and importantly, the collinearity level between our constructed maps and the wheat physical map is higher than that between the Con_map_Wang2014 and the physical map. The seed coat color QTL detected in both populations under multiple environments were on the region (745.73–760.14 Mbp) of the seed color gene R-B1/Tamyb10-B1 (TraesCS3B02G515900, 3B: 757,918,264–757,920,082 bp). The validated consensus map will be beneficial for QTL mapping, positional cloning, meta-QTL analysis and wheat breading.

scholarly journals Genetic Mapping by Sequencing More Precisely Detects Loci Responsible for Anaerobic Germination Tolerance in Rice

Plants ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 705
Author(s):  
John Carlos I. Ignacio ◽  
Maricris Zaidem ◽  
Carlos Casal ◽  
Shalabh Dixit ◽  
Tobias Kretzschmar ◽  
...  
Keyword(s):  
Genetic Basis ◽  
Snp Markers ◽  
Nucleotide Polymorphism ◽  
Rice Varieties ◽  
Single Nucleotide ◽  
Genotyping Platform ◽  
Anaerobic Germination ◽  
Direct Seeded ◽  
Mapping By Sequencing ◽  
Simple Sequence

Direct seeded rice (DSR) is a mainstay for planting rice in the Americas, and it is rapidly becoming more popular in Asia. It is essential to develop rice varieties that are suitable for this type of production system. ASD1, a landrace from India, possesses several traits desirable for direct-seeded fields, including tolerance to anaerobic germination (AG). To map the genetic basis of its tolerance, we examined a population of 200 F2:3 families derived from a cross between IR64 and ASD1 using the restriction site-associated DNA sequencing (RAD-seq) technology. This genotyping platform enabled the identification of 1921 single nucleotide polymorphism (SNP) markers to construct a high-resolution genetic linkage map with an average interval of 0.9 cM. Two significant quantitative trait loci (QTLs) were detected on chromosomes 7 and 9, qAG7 and qAG9, with LOD scores of 7.1 and 15.0 and R2 values of 15.1 and 29.4, respectively. Here, we obtained more precise locations of the QTLs than traditional simple sequence repeat and low-density SNP genotyping methods and may help further dissect the genetic factors of these QTLs.

scholarly journals Inheritance and linkage analysis of co-dominant SSR markers on the Z chromosome of the silkworm (Bombyx mori L.)

2008 ◽  
Vol 90 (2) ◽  
pp. 151-156 ◽  
Author(s):  
XUE-XIA MIAO ◽  
WEI-HUA LI ◽  
MU-WANG LI ◽  
YUN-PO ZHAO ◽  
XIAN-RU GUO ◽  
...  
Keyword(s):  
Linkage Map ◽  
Bombyx Mori ◽  
Ssr Markers ◽  
Positional Cloning ◽  
Z Chromosome ◽  
Pcr Marker ◽  
Backcross Population ◽  
In The Beginning ◽  
Simple Sequence ◽  
Visible Mutation

SummaryMicrosatellites or simple sequence repeats (SSRs) are co-dominant molecular markers. When we used fluorescent SSR markers to construct a linkage map for the female heterogametic silkworm (Bombyx mori, ZW), we found that some loci did not segregate in a Mendelian ratio of 1:1 in a backcross population. These loci segregated in a 3:1 ratio of single bands compared with double bands. Further examination of band patterns indicated that three types of SSR bands were present: two homozygotes and one heterozygote. In the beginning, we considered to discard these markers. By scoring male and female F1 individuals, we confirmed that these loci were located on the Z chromosome. Using the sex-linked visible mutation sch (K05) and its wild-type (C108), we constructed an F1 male backcross (BC1M) mapping population. The combination of sch backcross and SSR data enabled us to map the SSR markers to the Z chromosome. By adjusting input parameters based on these data, we were able to use Mapmaker software to construct a linkage map. This strategy takes advantage of co-dominant markers for positional cloning of genes on the Z chromosome. We localized sch to the Z chromosome relative to six SSR markers and one PCR marker, covering a total of 76·1 cM. The sch mutation is an important sex-linked visible mutation widely used in breeding of commercial silkworms (e.g. male silkworm selection rearing). Localization of the sch gene may prove helpful in cloning the gene and developing strains for marker-assisted selection in silkworm breeding.

Linking porcine microsatellite markers to known genome regions by identifying their human orthologs

Genome ◽  
2003 ◽  
Vol 46 (5) ◽  
pp. 798-808 ◽  
Author(s):  
Zhihua Jiang ◽  
Jennifer J Michal
Keyword(s):  
Microsatellite Markers ◽  
Positional Cloning ◽  
Genome Mapping ◽  
Joint Analysis ◽  
Porcine Genome ◽  
Gene Markers ◽  
Human Orthologs ◽  
Human Genomic ◽  
Rh Panel ◽  
Simple Sequence

Microsatellites, or tandem simple sequence repeats (SSRs), have become one of the most popular molecular markers in genome mapping because of their abundance across genomes and because of their high levels of polymorphism. However, information on which genes surround or flank them has remained very limited for most SSRs, especially in livestock species. In this study, an in silico comparative mapping approach was developed to link porcine SSRs to known genome regions by identifying their human orthologs. From a total of 1321 porcine microsatellites used in this study, 228 were found to have blocks in alignment with human genomic sequences. These 228 SSRs span about 1459 cM of the porcine genome, but with uneven distributions, ranging from 2 on SSC12 to 24 on SSC14. Linking these porcine SSRs to the known genome regions in the human genome also revealed 16 new putative synteny groups between these two species. Fifteen SSRs on SSC3 with identified human orthologs were typed on a pig-hamster radiation hybrid (RH) panel and used in a joint analysis with 80 known gene markers previously mapped on SSC3 using the same panel. The analysis revealed that they were all highly linked to either one or both adjacent markers. These results indicated that assigning the porcine SSRs to known genome regions by identifying their human orthologs is a reliable approach. The process will provide a foundation for positional cloning of causative genes for economically important traits.Key words: pig, microsatellite markers, human orthologs, RH mapping.

scholarly journals In-vitro Antioxidant Capacities and Genetic Classification of Indonesian Selected Pigmented Rice

2021 ◽  
pp. 107
Author(s):  
Keyword(s):  
Simple Sequence Repeat ◽  
Ssr Marker ◽  
Radical Scavenging ◽  
Free Radical Scavenging ◽  
Genetic Classification ◽  
Pigmented Rice ◽  
The Relationship ◽  
Simple Sequence

Rice is a world-famous cereal food divided into pigmented and non-pigmented rice. Pigmented rice is popular as healthier food than non-pigmented rice due to its potency as an antioxidant. Nevertheless, the potential of pigmented rice has not been widely studied. Indonesian selected pigmented rice protein’s antioxidant potential and the non-protein compound were in-vitro studied. The antioxidant potencies were evaluated by extracting fresh seeds of nine pigmented rice (Aek Sibundong, Beureum Taleus, Gogo Niti-2, Lamongan-1, Merah SP, Merah Wangi, Mota, Ketan Hitam-2, and Super Manggis) and non-pigmented rice (IR-64) as control. Various free radical scavenging methods to determine the antioxidant activity (ABTS•+, DPPH•, OH• and O2-) were conducted. Meanwhile, the genetic classification was performed by a simple sequence repeat (SSR) marker to determine the relationship between varieties. The results showed that protein of Ketan Hitam-2 had the highest ABTS•+ radical scavenging (98.06%), followed by Beureum Taleus (42.54%). Ketan Hitam-2 protein also showed the highest OH• and O2- activities (43.49% and 6.02%, respectively). The highest DPPH• potency of the non-protein compounds also shown by Ketan Hitam-2 (32.23%) with the activity of OH• and O2- (20.63% and 14.56%, respectively). These results showed that Ketan Hitam-2 has the highest potency as an antioxidant, which could be recommended as a nutraceuticals compound.

scholarly journals ANALISIS KERAGAMAN GENETIK PLASMA NUTFAH KAKAO (Theobroma cacaoL.) BERDASARKANMARKA SSR / Analysis of Genetic Variability Germplasm of Cacao (Theobroma cacaoL.)Basedon SSR Marker

2020 ◽  
Vol 17 (4) ◽  
pp. 156
Author(s):  
Surti Kurniasih ◽  
Rubiyo Rubiyo ◽  
Asep Setiawan ◽  
Agus Purwantara ◽  
Sudarsono Sudarsono
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Ssr Markers ◽  
Theobroma Cacao ◽  
Simple Sequence Repeat ◽  
Ssr Marker ◽  
Gene Diversity ◽  
Sequence Repeat ◽  
Theobroma Cacao L ◽  
Simple Sequence

<p>Microsatellite or simple sequence repeat (SSR) markers have proven to be an excellent tool for cultivar identification, pedigree analysis, and genetic distance evaluations among organisms. The objectives of this research were to characterize cacao collection of Indonesian Coffee and Cacao Research Institute (ICCRI) and to analyze their genetic diversity using SSR markers. In this research, 39 SSR primer pairs were used to amplify genomic DNA of 29 cacao clones. Amplified SSR fragments for each primer pair were scored as individual band and used to determine genetic distance among evaluated cacao clones. Results of the experiment indicated that all SSR primer pairs evaluated were able to produce SSR markers for 29 cacao clones. The results also indicated that 34 out of 39 microsatellite loci evaluated were polymorphic, while 5 others were monomorphic. The total number of observed alleles among 29 clones was 132. Number of alleles per locus ranged from 4-8, with an average of 5.5 alelles per locus. Results of data analysis indicated that the PIC value was 0.665, the observed heterozigosity (Ho) was 0.651, and the gene diversity (He) was 0.720. The PIC, Ho, and He values were considered high. Genetic distances were evaluated using NTSys version 2.1 and dendrogram was constructed. Results of analysis indicated that 12 cacao clones evaluated were clustered in the first group with diversity coefficient of &lt; 3.75. Nine cacao clones were in the second group but with the same value of diversity coefficient (&lt;7.50). The rest of the cacao clones were in the third group with diversity coefficient of&gt;7.50. Based on those finding, all SSR primer pairs evaluated could be used to analyze cacao genome and be useful for genetic diversity analysis of cacao germplasm. The SSR marker analysis in ICCRI cacao collections resulted in high PIC, high observed heterozygosity, and high genetic diversity.</p><p>Key words: Theobroma cacao L, microsatelite, molecular marker, genetic diversity, heterozygosity</p><p> </p><p><strong>Abstrak</strong></p><p>Marka mikrosatelit atau sekuens sederhana berulang (simple sequence repeat = SSR) terbukti merupakan alat yang bagus untuk identifikasi kultivar, analisis pedigree, dan evaluasi jarak genetik berbagai organisme. Penelitian ini bertujuan untuk:1) karakterisasi kakao koleksi Pusat penelitian Kopi dan Kakao Indonesia menggunakan marka SSR dan 2) analisis keragaman genetik klon-klon kakao koleksi dengan menggunakan marka SSR. Dalam penelitian ini, 39 pasangan primer SSR telah digunakan untuk amplifikasi DNA genomik dari 29 klon kakao. Skoring pita SSR hasil amplifikasi menggunakan masing-masing pasangan primer dilakukan secara terpisah dan digunakan untuk menentukan jarak genetik di antara klon kakao yang dievaluasi. Hasil percobaan menunjukkan bahwa semua pasangan primer SSR yang digunakan mampu menghasilkan pita DNA hasil amplifikasi (marka SSR) untuk 29 klon kakao yang diuji. Hasil penelitian juga menunjukkan bahwa 34 dari 39 lokus SSR yang dianalisis bersifat polimorfik sedangkan lima primer yang lain bersifat monomorfik. Dari 29 klon kakao yang dievaluasi, telah berhasil diamplifikasi sebanyak 132 alel, dengan kisaran antara 4-8 alel/lokus. Rataan jumlah alel per lokus sebanyak 5,50. Hasil analisis data yang dilakukan juga menunjukkan nilai PIC untuk marka SSR yang digunakan sebesar 0,665. Untuk populasi klon kakao yang dievaluasi, diperoleh nilai rataan heterosigositas pengamatan (Ho) sebesar 0,651 dan rataan diversitas gen (He) sebesar 0,720. Nilai PIC Ho dan He yang didapat tergolong tinggi. Berdasarkan analisis keragaman dengan menggunakan program NTSys, diperoleh hasil 12 klon kakao berada dalam grup pertama (koefisien keragaman&lt;3,75) dan9 klon berada dalam grup kedua, dengan koefisien keragaman &lt; 7,50. Sedangkan klon-klon lainnya mempunyai koefisien keragaman &gt; 7,50. Berdasarkan hasil penelitian dan analisis data disimpulkan bahwa marka SSR dapat digunakan untuk menganalisis keragaman genetik plasma nutfah kakao. Tingkat polimorfisme yang dihasilkan marka SSR relatif tinggi. Tingkat heterosigositas plasma nutfah kakao koleksi Puslit Kopi dan Kakao Indonesiarelatif tinggi, dan keragaman genetiknyacukup tinggi.</p><p>Kata kunci : Theobroma cacao L, mikrosatelit, marka molekuler, keragaman genetik, heterosigositas</p>

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