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Journal articles on the topic 'Nested Association Mapping'

Author: Grafiati

Published: 4 June 2021

Last updated: 5 February 2022

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1

Guo, Baohong, David A. Sleper, and William D. Beavis. "Nested Association Mapping for Identification of Functional Markers." Genetics 186, no. 1 (2010): 373–83. http://dx.doi.org/10.1534/genetics.110.115782.

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2

McMullen, M. D., S. Kresovich, H. S. Villeda, et al. "Genetic Properties of the Maize Nested Association Mapping Population." Science 325, no. 5941 (2009): 737–40. http://dx.doi.org/10.1126/science.1174320.

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3

Fragoso, Christopher A., Maria Moreno, Zuoheng Wang, et al. "Genetic Architecture of a Rice Nested Association Mapping Population." G3: Genes|Genomes|Genetics 7, no. 6 (2017): 1913–26. http://dx.doi.org/10.1534/g3.117.041608.

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4

Nice, Liana M., Brian J. Steffenson, Thomas K. Blake, Richard D. Horsley, Kevin P. Smith, and Gary J. Muehlbauer. "Mapping Agronomic Traits in a Wild Barley Advanced Backcross-Nested Association Mapping Population." Crop Science 57, no. 3 (2017): 1199–210. http://dx.doi.org/10.2135/cropsci2016.10.0850.

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5

McCauley, DJ. "A Nested Association Mapping Population for Wheat Stem Rust Resistance." CSA News 65, no. 8 (2020): 6–9. http://dx.doi.org/10.1002/csan.20240.

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6

Guo, Baohong, and William D. Beavis. "In silico genotyping of the maize nested association mapping population." Molecular Breeding 27, no. 1 (2010): 107–13. http://dx.doi.org/10.1007/s11032-010-9503-4.

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7

Grover, Sajjan, Braden Wojahn, Suresh Varsani, Scott E. Sattler, and Joe Louis. "Resistance to greenbugs in the sorghum nested association mapping population." Arthropod-Plant Interactions 13, no. 2 (2019): 261–69. http://dx.doi.org/10.1007/s11829-019-09679-y.

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8

Brock, Marcus T., Matthew J. Rubin, Dean DellaPenna, and Cynthia Weinig. "A Nested Association Mapping Panel in Arabidopsis thaliana for Mapping and Characterizing Genetic Architecture." G3: Genes|Genomes|Genetics 10, no. 10 (2020): 3701–8. http://dx.doi.org/10.1534/g3.120.401239.

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Linkage and association mapping populations are crucial public resources that facilitate the characterization of trait genetic architecture in natural and agricultural systems. We define a large nested association mapping panel (NAM) from 14 publicly available recombinant inbred line populations (RILs) of Arabidopsis thaliana, which share a common recurrent parent (Col-0). Using a genotype-by-sequencing approach (GBS), we identified single nucleotide polymorphisms (SNPs; range 563-1525 per population) and subsequently built updated linkage maps in each of the 14 RIL sets. Simulations in indivi

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9

Kitony, Justine K., Hidehiko Sunohara, Mikako Tasaki, et al. "Development of an Aus-Derived Nested Association Mapping (Aus-NAM) Population in Rice." Plants 10, no. 6 (2021): 1255. http://dx.doi.org/10.3390/plants10061255.

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A genetic resource for studying genetic architecture of agronomic traits and environmental adaptation is essential for crop improvements. Here, we report the development of a rice nested association mapping population (aus-NAM) using 7 aus varieties as diversity donors and T65 as the common parent. Aus-NAM showed broad phenotypic variations. To test whether aus-NAM was useful for quantitative trait loci (QTL) mapping, known flowering genes (Ehd1, Hd1, and Ghd7) in rice were characterized using single-family QTL mapping, joint QTL mapping, and the methods based on genome-wide association study

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10

Blake, N. K., M. Pumphrey, K. Glover, et al. "Registration of the Triticeae-CAP Spring Wheat Nested Association Mapping Population." Journal of Plant Registrations 13, no. 2 (2019): 294–97. http://dx.doi.org/10.3198/jpr2018.07.0052crmp.

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11

Yu, Jianming, James B. Holland, Michael D. McMullen, and Edward S. Buckler. "Genetic Design and Statistical Power of Nested Association Mapping in Maize." Genetics 178, no. 1 (2008): 539–51. http://dx.doi.org/10.1534/genetics.107.074245.

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12

Zahn, Sebastian, Thomas Schmutzer, Klaus Pillen, and Andreas Maurer. "Genomic Dissection of Peduncle Morphology in Barley through Nested Association Mapping." Plants 10, no. 1 (2020): 10. http://dx.doi.org/10.3390/plants10010010.

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Straw biomass and stability are crucial for stable yields. Moreover, straw harbors the potential to serve as a valuable raw material for bio-economic processes. The peduncle is the top part of the last shoot internode and carries the spike. This study investigates the genetic control of barley peduncle morphology. Therefore, 1411 BC1S3 lines of the nested association mapping (NAM) population “Halle Exotic Barley 25” (HEB-25), generated by crossing the spring barley elite cultivar Barke with an assortment of 25 exotic barley accessions, were used. Applying 50k Illumina Infinium iSelect SNP geno

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13

Bajgain, Prabin, Yue Jin, Toi J. Tsilo, et al. "Registration of KUWNSr, a wheat stem rust nested association mapping population." Journal of Plant Registrations 14, no. 3 (2020): 467–73. http://dx.doi.org/10.1002/plr2.20043.

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14

Tian, Feng, Peter J. Bradbury, Patrick J. Brown, et al. "Genome-wide association study of leaf architecture in the maize nested association mapping population." Nature Genetics 43, no. 2 (2011): 159–62. http://dx.doi.org/10.1038/ng.746.

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15

Olatoye, Marcus O., Sandeep R. Marla, Zhenbin Hu, Sophie Bouchet, Ramasamy Perumal, and Geoffrey P. Morris. "Dissecting Adaptive Traits with Nested Association Mapping: Genetic Architecture of Inflorescence Morphology in Sorghum." G3: Genes|Genomes|Genetics 10, no. 5 (2020): 1785–96. http://dx.doi.org/10.1534/g3.119.400658.

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In the cereal crop sorghum (Sorghum bicolor) inflorescence morphology variation underlies yield variation and confers adaptation across precipitation gradients, but its genetic basis is poorly understood. We characterized the genetic architecture of sorghum inflorescence morphology using a global nested association mapping (NAM) population (2200 recombinant inbred lines) and 198,000 phenotypic observations from multi-environment trials for four inflorescence morphology traits (upper branch length, lower branch length, rachis length, and rachis diameter). Trait correlations suggest that lower a

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16

Cook, Jason P., Michael D. McMullen, James B. Holland, et al. "Genetic Architecture of Maize Kernel Composition in the Nested Association Mapping and Inbred Association Panels." Plant Physiology 158, no. 2 (2011): 824–34. http://dx.doi.org/10.1104/pp.111.185033.

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17

Zhang, Nengyi, Yves Gibon, Jason G. Wallace, et al. "Genome-Wide Association of Carbon and Nitrogen Metabolism in the Maize Nested Association Mapping Population." Plant Physiology 168, no. 2 (2015): 575–83. http://dx.doi.org/10.1104/pp.15.00025.

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18

Beche, Eduardo, Jason D. Gillman, Qijian Song, et al. "Nested association mapping of important agronomic traits in three interspecific soybean populations." Theoretical and Applied Genetics 133, no. 3 (2020): 1039–54. http://dx.doi.org/10.1007/s00122-019-03529-4.

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19

Guo, Zhigang, Dominic M. Tucker, Jianwei Lu, Venkata Kishore, and Gilles Gay. "Evaluation of genome-wide selection efficiency in maize nested association mapping populations." Theoretical and Applied Genetics 124, no. 2 (2011): 261–75. http://dx.doi.org/10.1007/s00122-011-1702-9.

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20

Perumal, Ramasamy, Tesfaye T. Tesso, Geoffrey P. Morris, et al. "Registration of the sorghum nested association mapping (NAM) population in RTx430 background." Journal of Plant Registrations 15, no. 2 (2021): 395–402. http://dx.doi.org/10.1002/plr2.20110.

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21

Kidane, Yosef G., Cherinet A. Gesesse, Bogale N. Hailemariam, et al. "A large nested association mapping population for breeding and quantitative trait locus mapping in Ethiopian durum wheat." Plant Biotechnology Journal 17, no. 7 (2019): 1380–93. http://dx.doi.org/10.1111/pbi.13062.

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22

Guo, Zhigang, Dominic M. Tucker, Daolong Wang, et al. "Accuracy of Across-Environment Genome-Wide Prediction in Maize Nested Association Mapping Populations." G3: Genes|Genomes|Genetics 3, no. 2 (2013): 263–72. http://dx.doi.org/10.1534/g3.112.005066.

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23

Bajgain, Prabin, Matthew N. Rouse, Toi J. Tsilo, et al. "Nested Association Mapping of Stem Rust Resistance in Wheat Using Genotyping by Sequencing." PLOS ONE 11, no. 5 (2016): e0155760. http://dx.doi.org/10.1371/journal.pone.0155760.

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24

Chen, Qiuyue, Chin Jian Yang, Alessandra M. York, et al. "TeoNAM: A Nested Association Mapping Population for Domestication and Agronomic Trait Analysis in Maize." Genetics 213, no. 3 (2019): 1065–78. http://dx.doi.org/10.1534/genetics.119.302594.

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25

Stich, Benjamin. "Comparison of Mating Designs for Establishing Nested Association Mapping Populations in Maize andArabidopsis thaliana." Genetics 183, no. 4 (2009): 1525–34. http://dx.doi.org/10.1534/genetics.109.108449.

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26

Poland, J. A., P. J. Bradbury, E. S. Buckler, and R. J. Nelson. "Genome-wide nested association mapping of quantitative resistance to northern leaf blight in maize." Proceedings of the National Academy of Sciences 108, no. 17 (2011): 6893–98. http://dx.doi.org/10.1073/pnas.1010894108.

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27

Gage, Joseph L., Brandon Monier, Anju Giri, and Edward S. Buckler. "Ten Years of the Maize Nested Association Mapping Population: Impact, Limitations, and Future Directions." Plant Cell 32, no. 7 (2020): 2083–93. http://dx.doi.org/10.1105/tpc.19.00951.

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28

Marla, Sandeep R., Gloria Burow, Ratan Chopra, et al. "Genetic Architecture of Chilling Tolerance in Sorghum Dissected with a Nested Association Mapping Population." G3: Genes|Genomes|Genetics 9, no. 12 (2019): 4045–57. http://dx.doi.org/10.1534/g3.119.400353.

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29

Gireesh, Channappa, Raman M. Sundaram, Siddaiah M. Anantha, et al. "Nested Association Mapping (NAM) Populations: Present Status and Future Prospects in the Genomics Era." Critical Reviews in Plant Sciences 40, no. 1 (2021): 49–67. http://dx.doi.org/10.1080/07352689.2021.1880019.

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30

Kump, Kristen L., Peter J. Bradbury, Randall J. Wisser, et al. "Genome-wide association study of quantitative resistance to southern leaf blight in the maize nested association mapping population." Nature Genetics 43, no. 2 (2011): 163–68. http://dx.doi.org/10.1038/ng.747.

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31

Scott, Kelsey, Christine Balk, Deloris Veney, Leah K. McHale, and Anne E. Dorrance. "Quantitative Disease Resistance Loci towardsPhytophthora sojaeand Three Species ofPythiumin Six Soybean Nested Association Mapping Populations." Crop Science 59, no. 2 (2019): 605–23. http://dx.doi.org/10.2135/cropsci2018.09.0573.

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32

Wang, Xiaoqian, Luhao Dong, Junmei Hu, et al. "Dissecting genetic loci affecting grain morphological traits to improve grain weight via nested association mapping." Theoretical and Applied Genetics 132, no. 11 (2019): 3115–28. http://dx.doi.org/10.1007/s00122-019-03410-4.

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33

Stich, Benjamin, H. Friedrich Utz, Hans-Peter Piepho, Hans P. Maurer, and Albrecht E. Melchinger. "Optimum allocation of resources for QTL detection using a nested association mapping strategy in maize." Theoretical and Applied Genetics 120, no. 3 (2009): 553–61. http://dx.doi.org/10.1007/s00122-009-1175-2.

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34

Bian, Yang, Qin Yang, Peter J. Balint-Kurti, Randall J. Wisser, and James B. Holland. "Limits on the reproducibility of marker associations with southern leaf blight resistance in the maize nested association mapping population." BMC Genomics 15, no. 1 (2014): 1068. http://dx.doi.org/10.1186/1471-2164-15-1068.

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35

Bouchet, Sophie, Marcus O. Olatoye, Sandeep R. Marla, et al. "Increased Power To Dissect Adaptive Traits in Global Sorghum Diversity Using a Nested Association Mapping Population." Genetics 206, no. 2 (2017): 573–85. http://dx.doi.org/10.1534/genetics.116.198499.

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36

Sharma, Rajiv, Fulvia Draicchio, Hazel Bull, et al. "Genome-wide association of yield traits in a nested association mapping population of barley reveals new gene diversity for future breeding." Journal of Experimental Botany 69, no. 16 (2018): 3811–22. http://dx.doi.org/10.1093/jxb/ery178.

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37

Jordan, Katherine W., Shichen Wang, Fei He, et al. "The genetic architecture of genome‐wide recombination rate variation in allopolyploid wheat revealed by nested association mapping." Plant Journal 95, no. 6 (2018): 1039–54. http://dx.doi.org/10.1111/tpj.14009.

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38

Ali, Muhammad Jaffer, Guangnan Xing, Jianbo He, Tuanjie Zhao, and Junyi Gai. "Detecting the QTL-allele system controlling seed-flooding tolerance in a nested association mapping population of soybean." Crop Journal 8, no. 5 (2020): 781–92. http://dx.doi.org/10.1016/j.cj.2020.06.008.

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39

Nice, Liana M., Brian J. Steffenson, Gina L. Brown-Guedira, et al. "Development and Genetic Characterization of an Advanced Backcross-Nested Association Mapping (AB-NAM) Population of Wild × Cultivated Barley." Genetics 203, no. 3 (2016): 1453–67. http://dx.doi.org/10.1534/genetics.116.190736.

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40

Hung, H.-Y., C. Browne, K. Guill, et al. "The relationship between parental genetic or phenotypic divergence and progeny variation in the maize nested association mapping population." Heredity 108, no. 5 (2011): 490–99. http://dx.doi.org/10.1038/hdy.2011.103.

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41

Andrade, Luciano Rogério Braatz de, Roberto Fritsche Neto, Ítalo Stefanine Correia Granato, Gustavo César Sant’Ana, Pedro Patric Pinho Morais, and Aluízio Borém. "Genetic Vulnerability and the Relationship of Commercial Germplasms of Maize in Brazil with the Nested Association Mapping Parents." PLOS ONE 11, no. 10 (2016): e0163739. http://dx.doi.org/10.1371/journal.pone.0163739.

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42

Maurer, Andreas, Vera Draba, and Klaus Pillen. "Genomic dissection of plant development and its impact on thousand grain weight in barley through nested association mapping." Journal of Experimental Botany 67, no. 8 (2016): 2507–18. http://dx.doi.org/10.1093/jxb/erw070.

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43

Herzig, Paul, Andreas Maurer, Vera Draba, et al. "Contrasting genetic regulation of plant development in wild barley grown in two European environments revealed by nested association mapping." Journal of Experimental Botany 69, no. 7 (2018): 1517–31. http://dx.doi.org/10.1093/jxb/ery002.

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44

Gangurde, Sunil S., Hui Wang, Shasidhar Yaduru, et al. "Nested‐association mapping (NAM)‐based genetic dissection uncovers candidate genes for seed and pod weights in peanut ( Arachis hypogaea )." Plant Biotechnology Journal 18, no. 6 (2019): 1457–71. http://dx.doi.org/10.1111/pbi.13311.

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45

Vollrath, Paul, Harmeet S. Chawla, Sarah V. Schiessl, et al. "A novel deletion in FLOWERING LOCUS T modulates flowering time in winter oilseed rape." Theoretical and Applied Genetics 134, no. 4 (2021): 1217–31. http://dx.doi.org/10.1007/s00122-021-03768-4.

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Abstract Key message A novel structural variant was discovered in the FLOWERING LOCUS T orthologue BnaFT.A02 by long-read sequencing. Nested association mapping in an elite winter oilseed rape population revealed that this 288 bp deletion associates with early flowering, putatively by modification of binding-sites for important flowering regulation genes. Abstract Perfect timing of flowering is crucial for optimal pollination and high seed yield. Extensive previous studies of flowering behavior in Brassica napus (canola, rapeseed) identified mutations in key flowering regulators which differen

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46

Hufford, Matthew B., Arun S. Seetharam, Margaret R. Woodhouse, et al. "De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes." Science 373, no. 6555 (2021): 655–62. http://dx.doi.org/10.1126/science.abg5289.

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We report de novo genome assemblies, transcriptomes, annotations, and methylomes for the 26 inbreds that serve as the founders for the maize nested association mapping population. The number of pan-genes in these diverse genomes exceeds 103,000, with approximately a third found across all genotypes. The results demonstrate that the ancient tetraploid character of maize continues to degrade by fractionation to the present day. Excellent contiguity over repeat arrays and complete annotation of centromeres revealed additional variation in major cytological landmarks. We show that combining struct

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47

Chu, Y., C. C. Holbrook, T. G. Isleib, et al. "Phenotyping and genotyping parents of sixteen recombinant inbred peanut populations." Peanut Science 45, no. 1 (2018): 1–11. http://dx.doi.org/10.3146/ps17-17.1.

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ABSTRACT In peanut (Arachis hypogaea L.), most agronomically important traits such as yield, disease resistance, and pod and kernel characteristics are quantitatively inherited. Phenotypic selection of these traits in peanut breeding programs can be augmented by marker-assisted selection. However, reliable associations between unambiguous genetic markers and phenotypic traits have to be established by genetic mapping prior to early generation marker-assisted selection. Previously, a nested association mapping (NAM) population of 16 recombinant inbred line populations (RILs) consisting 4870 lin

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48

Venkatesh, Tyamagondlu V., George G. Harrigan, Tim Perez, and Sherry Flint-Garcia. "Compositional Assessments of Key Maize Populations: B73 Hybrids of the Nested Association Mapping Founder Lines and Diverse Landrace Inbred Lines." Journal of Agricultural and Food Chemistry 63, no. 21 (2015): 5282–95. http://dx.doi.org/10.1021/acs.jafc.5b00208.

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49

Li, Shuguang, Yongce Cao, Jianbo He, Tuanjie Zhao, and Junyi Gai. "Detecting the QTL-allele system conferring flowering date in a nested association mapping population of soybean using a novel procedure." Theoretical and Applied Genetics 130, no. 11 (2017): 2297–314. http://dx.doi.org/10.1007/s00122-017-2960-y.

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50

Chidzanga, Charity, Delphine Fleury, Ute Baumann, et al. "Development of an Australian Bread Wheat Nested Association Mapping Population, a New Genetic Diversity Resource for Breeding under Dry and Hot Climates." International Journal of Molecular Sciences 22, no. 9 (2021): 4348. http://dx.doi.org/10.3390/ijms22094348.

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Genetic diversity, knowledge of the genetic architecture of the traits of interest and efficient means of transferring the desired genetic diversity into the relevant genetic background are prerequisites for plant breeding. Exotic germplasm is a rich source of genetic diversity; however, they harbor undesirable traits that limit their suitability for modern agriculture. Nested association mapping (NAM) populations are valuable genetic resources that enable incorporation of genetic diversity, dissection of complex traits and providing germplasm to breeding programs. We developed the OzNAM by cr

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