publication . Article . 2017

Incomplete dominance of deleterious alleles contributes substantially to trait variation and heterosis in maize

Yang, Jinliang; Mezmouk, Sofiane; Baumgarten, Andy; Buckler, Edward S.; Guill, Katherine E.; McMullen, Michael D.; Mumm, Rita H.; Ross-Ibarra, Jeffrey;
Open Access English
  • Published: 01 Sep 2017 Journal: PLoS Genetics, volume 13, issue 9 (issn: 1553-7390, eissn: 1553-7404, Copyright policy)
  • Publisher: Public Library of Science
Abstract
Deleterious alleles have long been proposed to play an important role in patterning phenotypic variation and are central to commonly held ideas explaining the hybrid vigor observed in the offspring of a cross between two inbred parents. We test these ideas using evolutionary measures of sequence conservation to ask whether incorporating information about putatively deleterious alleles can inform genomic selection (GS) models and improve phenotypic prediction. We measured a number of agronomic traits in both the inbred parents and hybrids of an elite maize partial diallel population and re-sequenced the parents of the population. Inbred elite maize lines vary for...
Subjects
free text keywords: Molecular Biology, Biotechnology, Research Article, Plant Biotechnology, Mathematics, Eukaryota, Inbreeding, Mathematical and Statistical Techniques, Genetic Loci, QH426-470, Genetics, Grasses, Physical Sciences, Plants, Heterosis, Genomics, Plant Science, Experimental Organism Systems, Alleles, Molecular Genetics, Statistics (Mathematics), Biology and Life Sciences, Forecasting, Research and Analysis Methods, Plant Genomics, Heredity, Maize, Plant and Algal Models, Plant Genetics, Phenotypes, Model Organisms, Organisms, Statistical Methods
Funded by
NSF| Genetic Architecture of Maize and Teosinte
Project
  • Funder: National Science Foundation (NSF)
  • Project Code: 0820619
  • Funding stream: Directorate for Biological Sciences | Division of Integrative Organismal Systems
,
NSF| Biology of Rare Alleles in Maize and Its Wild Relatives
Project
  • Funder: National Science Foundation (NSF)
  • Project Code: 1238014
  • Funding stream: Directorate for Biological Sciences | Division of Integrative Organismal Systems
72 references, page 1 of 5

a 60− e 0 . 5 ed 06 lianp .54exE 60− e ce .40 n a 6 i 0 r eaV .35

1. Timothy Mathes Beissinger, Li Wang, Kate Crosby, Arun Durvasula, Matthew B Hufford, and Jeffrey Ross-Ibarra. Recent demography drives changes in linked selection across the maize genome. Nature Plants, 2(7):16084, 2016. ISSN 2055-0278. doi: 10.1038/nplants.2016.84. URL http://www.ncbi.nlm.nih.gov/pubmed/27294617$\ delimiter"026E30F$nhttp://www.nature.com/articles/nplants201684.

2. James A Birchler, Donald L Auger, and Nicole C Riddle. In search of the molecular basis of heterosis. The Plant Cell, 15(10):2236{2239, 2003.

3. James A Birchler, Hong Yao, Sivanandan Chudalayandi, Daniel Vaiman, and Reiner A Veitia. Heterosis. The Plant Cell, 22(7):2105{2112, 2010.

4. Brian L Browning and Sharon R Browning. A unified approach to genotype imputation and haplotype-phase inference for large data sets of trios and unrelated individuals. Am J Hum Genet, 84(2):210{23, Feb 2009. doi: 10.1016/j.ajhg.2009.01.005.

5. Edward S Buckler, James B Holland, Peter J Bradbury, Charlotte B Acharya, Patrick J Brown, Chris Browne, Elhan Ersoz, Sherry Flint-Garcia, Arturo Garcia, Jeffrey C Glaubitz, et al. The genetic architecture of maize flowering time. Science, 325(5941):714{718, 2009. [OpenAIRE]

6. Robert Bukowski, Xiaosen Guo, Yanli Lu, Cheng Zou, Bing He, Zhengqin Rong, Bo Wang, Dawen Xu, Bicheng Yang, Chuanxiao Xie, et al. Construction of the third generation zea mays haplotype map. bioRxiv, page 026963, 2015.

7. Deborah Charlesworth and John H Willis. The genetics of inbreeding depression. Nature reviews. Genetics, 10(11):783{96, November 2009. ISSN 1471-0064. doi: 10.1038/nrg2664. URL http://www.ncbi.nlm.nih.gov/pubmed/19834483.

8. Jer-Ming Chia, Chi Song, Peter J Bradbury, Denise Costich, Natalia de Leon, John Doebley, Robert J Elshire, Brandon Gaut, Laura Geller, Jeffrey C Glaubitz, Michael Gore, Kate E Guill, Jim Holland, Matthew B Hufford, Jinsheng Lai, Meng Li, Xin Liu, Yanli Lu, Richard McCombie, Rebecca Nelson, Jesse Poland, Boddupalli M Prasanna, Tanja Pyhajarvi, Tingzhao Rong, Rajandeep S Sekhon, Qi Sun, Maud I Tenaillon, Feng Tian, Jun Wang, Xun Xu, Zhiwu Zhang, Shawn M Kaeppler, Jeffrey Ross-Ibarra, Michael D McMullen, Edward S Buckler, Gengyun Zhang, Yunbi Xu, and Doreen Ware. Maize hapmap2 identifies extant variation from a genome in flux. Nat Genet, 44(7):803{7, Jul 2012. doi: 10.1038/ng.2313.

9. P. Cingolani, A. Platts, M. Coon, T. Nguyen, L. Wang, S.J. Land, X. Lu, and D.M. Ruden. A program for annotating and predicting the effects of single nucleotide polymorphisms, snpeff: Snps in the genome of drosophila melanogaster strain w1118; iso-2; iso-3. Fly, 6(2):80{92, 2012.

10. Gregory M Cooper, Eric a Stone, George Asimenos, Eric D Green, Serafim Batzoglou, and Arend Sidow. Distribution and intensity of constraint in mammalian genomic sequence. Genome research, 15(7):901{13, July 2005. ISSN 1088-9051. doi: 10.1101/gr.3577405. URL http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1172034& tool=pmcentrez&rendertype=abstract.

11. James F Crow. 90 years ago: the beginning of hybrid maize. Genetics, 148(3): 923{928, 1998.

12. James F Crow. 90 years ago: the beginning of hybrid maize. Genetics, 148(3): 923{928, 1998.

13. Yang Da, Chunkao Wang, Shengwen Wang, and Guo Hu. Mixed model methods for genomic prediction and variance component estimation of additive and dominance effects using snp markers. PloS one, 9(1), 2014.

14. Eugene V Davydov, David L Goode, Marina Sirota, Gregory M Cooper, Arend Sidow, and Serafim Batzoglou. Identifying a high fraction of the human genome to be under selective constraint using GERP++. PLoS computational biology, 6 (12):e1001025, January 2010. ISSN 1553-7358. doi: 10.1371/journal.pcbi.1001025. URL http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid= 2996323&tool=pmcentrez&rendertype=abstract. [OpenAIRE]

72 references, page 1 of 5
Abstract
Deleterious alleles have long been proposed to play an important role in patterning phenotypic variation and are central to commonly held ideas explaining the hybrid vigor observed in the offspring of a cross between two inbred parents. We test these ideas using evolutionary measures of sequence conservation to ask whether incorporating information about putatively deleterious alleles can inform genomic selection (GS) models and improve phenotypic prediction. We measured a number of agronomic traits in both the inbred parents and hybrids of an elite maize partial diallel population and re-sequenced the parents of the population. Inbred elite maize lines vary for...
Subjects
free text keywords: Molecular Biology, Biotechnology, Research Article, Plant Biotechnology, Mathematics, Eukaryota, Inbreeding, Mathematical and Statistical Techniques, Genetic Loci, QH426-470, Genetics, Grasses, Physical Sciences, Plants, Heterosis, Genomics, Plant Science, Experimental Organism Systems, Alleles, Molecular Genetics, Statistics (Mathematics), Biology and Life Sciences, Forecasting, Research and Analysis Methods, Plant Genomics, Heredity, Maize, Plant and Algal Models, Plant Genetics, Phenotypes, Model Organisms, Organisms, Statistical Methods
Funded by
NSF| Genetic Architecture of Maize and Teosinte
Project
  • Funder: National Science Foundation (NSF)
  • Project Code: 0820619
  • Funding stream: Directorate for Biological Sciences | Division of Integrative Organismal Systems
,
NSF| Biology of Rare Alleles in Maize and Its Wild Relatives
Project
  • Funder: National Science Foundation (NSF)
  • Project Code: 1238014
  • Funding stream: Directorate for Biological Sciences | Division of Integrative Organismal Systems
72 references, page 1 of 5

a 60− e 0 . 5 ed 06 lianp .54exE 60− e ce .40 n a 6 i 0 r eaV .35

1. Timothy Mathes Beissinger, Li Wang, Kate Crosby, Arun Durvasula, Matthew B Hufford, and Jeffrey Ross-Ibarra. Recent demography drives changes in linked selection across the maize genome. Nature Plants, 2(7):16084, 2016. ISSN 2055-0278. doi: 10.1038/nplants.2016.84. URL http://www.ncbi.nlm.nih.gov/pubmed/27294617$\ delimiter"026E30F$nhttp://www.nature.com/articles/nplants201684.

2. James A Birchler, Donald L Auger, and Nicole C Riddle. In search of the molecular basis of heterosis. The Plant Cell, 15(10):2236{2239, 2003.

3. James A Birchler, Hong Yao, Sivanandan Chudalayandi, Daniel Vaiman, and Reiner A Veitia. Heterosis. The Plant Cell, 22(7):2105{2112, 2010.

4. Brian L Browning and Sharon R Browning. A unified approach to genotype imputation and haplotype-phase inference for large data sets of trios and unrelated individuals. Am J Hum Genet, 84(2):210{23, Feb 2009. doi: 10.1016/j.ajhg.2009.01.005.

5. Edward S Buckler, James B Holland, Peter J Bradbury, Charlotte B Acharya, Patrick J Brown, Chris Browne, Elhan Ersoz, Sherry Flint-Garcia, Arturo Garcia, Jeffrey C Glaubitz, et al. The genetic architecture of maize flowering time. Science, 325(5941):714{718, 2009. [OpenAIRE]

6. Robert Bukowski, Xiaosen Guo, Yanli Lu, Cheng Zou, Bing He, Zhengqin Rong, Bo Wang, Dawen Xu, Bicheng Yang, Chuanxiao Xie, et al. Construction of the third generation zea mays haplotype map. bioRxiv, page 026963, 2015.

7. Deborah Charlesworth and John H Willis. The genetics of inbreeding depression. Nature reviews. Genetics, 10(11):783{96, November 2009. ISSN 1471-0064. doi: 10.1038/nrg2664. URL http://www.ncbi.nlm.nih.gov/pubmed/19834483.

8. Jer-Ming Chia, Chi Song, Peter J Bradbury, Denise Costich, Natalia de Leon, John Doebley, Robert J Elshire, Brandon Gaut, Laura Geller, Jeffrey C Glaubitz, Michael Gore, Kate E Guill, Jim Holland, Matthew B Hufford, Jinsheng Lai, Meng Li, Xin Liu, Yanli Lu, Richard McCombie, Rebecca Nelson, Jesse Poland, Boddupalli M Prasanna, Tanja Pyhajarvi, Tingzhao Rong, Rajandeep S Sekhon, Qi Sun, Maud I Tenaillon, Feng Tian, Jun Wang, Xun Xu, Zhiwu Zhang, Shawn M Kaeppler, Jeffrey Ross-Ibarra, Michael D McMullen, Edward S Buckler, Gengyun Zhang, Yunbi Xu, and Doreen Ware. Maize hapmap2 identifies extant variation from a genome in flux. Nat Genet, 44(7):803{7, Jul 2012. doi: 10.1038/ng.2313.

9. P. Cingolani, A. Platts, M. Coon, T. Nguyen, L. Wang, S.J. Land, X. Lu, and D.M. Ruden. A program for annotating and predicting the effects of single nucleotide polymorphisms, snpeff: Snps in the genome of drosophila melanogaster strain w1118; iso-2; iso-3. Fly, 6(2):80{92, 2012.

10. Gregory M Cooper, Eric a Stone, George Asimenos, Eric D Green, Serafim Batzoglou, and Arend Sidow. Distribution and intensity of constraint in mammalian genomic sequence. Genome research, 15(7):901{13, July 2005. ISSN 1088-9051. doi: 10.1101/gr.3577405. URL http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1172034& tool=pmcentrez&rendertype=abstract.

11. James F Crow. 90 years ago: the beginning of hybrid maize. Genetics, 148(3): 923{928, 1998.

12. James F Crow. 90 years ago: the beginning of hybrid maize. Genetics, 148(3): 923{928, 1998.

13. Yang Da, Chunkao Wang, Shengwen Wang, and Guo Hu. Mixed model methods for genomic prediction and variance component estimation of additive and dominance effects using snp markers. PloS one, 9(1), 2014.

14. Eugene V Davydov, David L Goode, Marina Sirota, Gregory M Cooper, Arend Sidow, and Serafim Batzoglou. Identifying a high fraction of the human genome to be under selective constraint using GERP++. PLoS computational biology, 6 (12):e1001025, January 2010. ISSN 1553-7358. doi: 10.1371/journal.pcbi.1001025. URL http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid= 2996323&tool=pmcentrez&rendertype=abstract. [OpenAIRE]

72 references, page 1 of 5
Powered by OpenAIRE Open Research Graph
Any information missing or wrong?Report an Issue
publication . Article . 2017

Incomplete dominance of deleterious alleles contributes substantially to trait variation and heterosis in maize

Yang, Jinliang; Mezmouk, Sofiane; Baumgarten, Andy; Buckler, Edward S.; Guill, Katherine E.; McMullen, Michael D.; Mumm, Rita H.; Ross-Ibarra, Jeffrey;