Insights into the Effects of Long-Term Artificial Selection on Seed Size in Maize. Issue 1 (17th July 2014)
- Record Type:
- Journal Article
- Title:
- Insights into the Effects of Long-Term Artificial Selection on Seed Size in Maize. Issue 1 (17th July 2014)
- Main Title:
- Insights into the Effects of Long-Term Artificial Selection on Seed Size in Maize
- Authors:
- Hirsch, Candice N
Flint-Garcia, Sherry A
Beissinger, Timothy M
Eichten, Steven R
Deshpande, Shweta
Barry, Kerrie
McMullen, Michael D
Holland, James B
Buckler, Edward S
Springer, Nathan
Buell, C Robin
de Leon, Natalia
Kaeppler, Shawn M - Abstract:
- Abstract: Grain produced from cereal crops is a primary source of human food and animal feed worldwide. To understand the genetic basis of seed-size variation, a grain yield component, we conducted a genome-wide scan to detect evidence of selection in the maize Krug Yellow Dent long-term divergent seed-size selection experiment. Previous studies have documented significant phenotypic divergence between the populations. Allele frequency estimates for ∼3 million single nucleotide polymorphisms (SNPs) in the base population and selected populations were estimated from pooled whole-genome resequencing of 48 individuals per population. Using F ST values across sliding windows, 94 divergent regions with a median of six genes per region were identified. Additionally, 2729 SNPs that reached fixation in both selected populations with opposing fixed alleles were identified, many of which clustered in two regions of the genome. Copy-number variation was highly prevalent between the selected populations, with 532 total regions identified on the basis of read-depth variation and comparative genome hybridization. Regions important for seed weight in natural variation were identified in the maize nested association mapping population. However, the number of regions that overlapped with the long-term selection experiment did not exceed that expected by chance, possibly indicating unique sources of variation between the two populations. The results of this study provide insights into theAbstract: Grain produced from cereal crops is a primary source of human food and animal feed worldwide. To understand the genetic basis of seed-size variation, a grain yield component, we conducted a genome-wide scan to detect evidence of selection in the maize Krug Yellow Dent long-term divergent seed-size selection experiment. Previous studies have documented significant phenotypic divergence between the populations. Allele frequency estimates for ∼3 million single nucleotide polymorphisms (SNPs) in the base population and selected populations were estimated from pooled whole-genome resequencing of 48 individuals per population. Using F ST values across sliding windows, 94 divergent regions with a median of six genes per region were identified. Additionally, 2729 SNPs that reached fixation in both selected populations with opposing fixed alleles were identified, many of which clustered in two regions of the genome. Copy-number variation was highly prevalent between the selected populations, with 532 total regions identified on the basis of read-depth variation and comparative genome hybridization. Regions important for seed weight in natural variation were identified in the maize nested association mapping population. However, the number of regions that overlapped with the long-term selection experiment did not exceed that expected by chance, possibly indicating unique sources of variation between the two populations. The results of this study provide insights into the genetic elements underlying seed-size variation in maize and could also have applications for other cereal crops. … (more)
- Is Part Of:
- Genetics. Volume 198:Issue 1(2014)
- Journal:
- Genetics
- Issue:
- Volume 198:Issue 1(2014)
- Issue Display:
- Volume 198, Issue 1 (2014)
- Year:
- 2014
- Volume:
- 198
- Issue:
- 1
- Issue Sort Value:
- 2014-0198-0001-0000
- Page Start:
- 409
- Page End:
- 421
- Publication Date:
- 2014-07-17
- Subjects:
- copy-number variation -- maize -- natural variation -- seed size -- selection signatures
Genetics -- Periodicals
576.5 - Journal URLs:
- http://www.oxfordjournals.org/ ↗
- DOI:
- 10.1534/genetics.114.167155 ↗
- Languages:
- English
- ISSNs:
- 0016-6731
- Deposit Type:
- Legaldeposit
- View Content:
- Available online (eLD content is only available in our Reading Rooms) ↗
- Physical Locations:
- British Library DSC - BLDSS-3PM
British Library HMNTS - ELD Digital store - Ingest File:
- 25435.xml