1
|
Prado JR, Segers G, Voelker T, Carson D, Dobert R, Phillips J, Cook K, Cornejo C, Monken J, Grapes L, Reynolds T, Martino-Catt S. Genetically engineered crops: from idea to product. Annu Rev Plant Biol 2014; 65:769-90. [PMID: 24579994 DOI: 10.1146/annurev-arplant-050213-040039] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Genetically engineered crops were first commercialized in 1994 and since then have been rapidly adopted, enabling growers to more effectively manage pests and increase crop productivity while ensuring food, feed, and environmental safety. The development of these crops is complex and based on rigorous science that must be well coordinated to create a plant with desired beneficial phenotypes. This article describes the general process by which a genetically engineered crop is developed from an initial concept to a commercialized product.
Collapse
|
2
|
Grapes L, Rothschild MF. Investigation of a QTL region for loin eye area and fatness on pig Chromosome 1. Mamm Genome 2006; 17:657-68. [PMID: 16783645 DOI: 10.1007/s00335-005-0188-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2005] [Accepted: 01/15/2006] [Indexed: 10/24/2022]
Abstract
Previously, quantitative trait loci (QTL) for tenth-rib backfat (TENTHRIB) and loin eye area (LEA) were identified on pig Chromosome 1 (SSC 1) near microsatellite S0008 from a three-generation Berkshire x Yorkshire cross (BY). This work attempted to refine these QTL positions and identify genes associated with these QTL. Genotypes of BY (n = 555) were determined by PCR-RFLP or PCR tests for 13 polymorphisms identified in BY F(0) individuals for candidate genes, BAC end sequences, and genomic clones. Using least-squares regression interval mapping, the LEA QTL was estimated at S0008; the TENTHRIB QTL position was shifted approximately 1 cM downstream from S0008. Of the genes/sequences mapped in the QTL region, CL349415 was significantly associated with TENTHRIB (p = 0.02) and solute carrier family 2, member 12 (SLC2A12) was significantly associated with LEA (p = 0.02). These results suggest that the gene(s) responsible for the LEA and TENTHRIB QTL effects are tightly linked to S0008 or that the high informativeness of S0008 relative to surrounding markers is influencing the QTL position estimates. In addition, janus kinase 2 (JAK2) was mapped to a suggestive LEA QTL region and showed association with LEA (p = 0.009), fatness, color, and pH traits in BY.
Collapse
Affiliation(s)
- Laura Grapes
- Department of Animal Science and Center for Integrated Animal Genomics, Iowa State University, 2255 Kildee Hall, Ames, IA 50011, USA
| | | |
Collapse
|
3
|
Hittmeier LJ, Grapes L, Lensing RL, Rothschild MF, Stahl CH. Genetic background influences metabolic response to dietary phosphorus restriction. J Nutr Biochem 2006; 17:385-95. [PMID: 16311027 DOI: 10.1016/j.jnutbio.2005.08.008] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2005] [Revised: 08/15/2005] [Accepted: 08/15/2005] [Indexed: 11/24/2022]
Abstract
Dietary phosphorus (P) is essential to bone growth and turnover; however, little research has focused on the genetic mechanisms controlling P utilization. Understanding the interactions between genetics and dietary P that optimize bone integrity could provide novel interventions for osteoporosis. Thirty-six pigs from two sire lines known to differ in bone structure [heavier boned (HB) and lighter boned (LB)] were assigned to one of the three diets (P adequate, P repletion or P deficient). After 14 days, bone marrow and intact radial bones were collected. Differences between these lines in growth rate, bone integrity and gene expression within bone marrow were observed. In HB, but not LB, pigs, the P-deficient diet decreased weight gain (P<.01). For both lines, P deficiency caused a reduction in radial bone strength (P<.01), but HB P-deficient animals had greater (P<.10) bone integrity than P-deficient LB pigs. In HB, but not LB, pigs, dietary treatment affected the expression of CALCR (calcitonin receptor) (P<.05), VDR (vitamin D receptor) (P<.04) and IGFBP3 (insulin-like growth factor binding protein 3) (P<.06). There was also a trend of increased IL6 (interleukin-6), TFIIB (transcription initiation factor IIB) and SOX9 (sex determining region Y-box 9) expression with P deficiency in HB, but not LB, pigs. Both genetic backgrounds responded similarly to P deficiency with an increase in the expression of OXTR (oxytocin receptor) and IGF1 (insulin-like growth factor 1). Differences in growth rate, bone integrity and gene expression within the bone marrow suggest a difference in the homeorhetic control of P utilization between these genetic lines. Understanding these differences could lead to novel treatments for osteoporosis and aid in the development of tests for identifying those at risk for this disease.
Collapse
Affiliation(s)
- Laura J Hittmeier
- Department of Animal Science and Center for Integrated Animal Genomics, Iowa State University, Ames, IA 50011, USA
| | | | | | | | | |
Collapse
|
4
|
Grapes L, Rudd S, Fernando RL, Megy K, Rocha D, Rothschild MF. Prospecting for pig single nucleotide polymorphisms in the human genome: have we struck gold? J Anim Breed Genet 2006; 123:145-51. [PMID: 16706918 DOI: 10.1111/j.1439-0388.2006.00587.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Gene-to-gene variation in the frequency of single nucleotide polymorphisms (SNPs) has been observed in humans, mice, rats, primates and pigs, but a relationship across species in this variation has not been described. Here, the frequency of porcine coding SNPs (cSNPs) identified by in silico methods, and the frequency of murine cSNPs, were compared with the frequency of human cSNPs across homologous genes. From 150,000 porcine expressed sequence tag (EST) sequences, a total of 452 SNP-containing sequence clusters were found, totalling 1394 putative SNPs. All the clustered porcine EST annotations and SNP data have been made publicly available at http://sputnik.btk.fi/project?name=swine. Human and murine cSNPs were identified from dbSNP and were characterized as either validated or total number of cSNPs (validated plus non-validated) for comparison purposes. The correlation between in silico pig cSNP and validated human cSNP densities was found to be 0.77 (p < 0.00001) for a set of 25 homologous genes, while a correlation of 0.48 (p < 0.0005) was found for a primarily random sample of 50 homologous human and mouse genes. This is the first evidence of conserved gene-to-gene variability in cSNP frequency across species and indicates that site-directed screening of porcine genes that are homologous to cSNP-rich human genes may rapidly advance cSNP discovery in pigs.
Collapse
Affiliation(s)
- L Grapes
- Department of Animal Science and Center for Integrated Animal Genomics, Iowa State University, Ames, IA 50011, USA
| | | | | | | | | | | |
Collapse
|
5
|
Grapes L, Firat MZ, Dekkers JCM, Rothschild MF, Fernando RL. Optimal haplotype structure for linkage disequilibrium-based fine mapping of quantitative trait loci using identity by descent. Genetics 2005; 172:1955-65. [PMID: 16322505 PMCID: PMC1456285 DOI: 10.1534/genetics.105.048686] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A linkage disequilibrium-based method for fine mapping quantitative trait loci (QTL) has been described that uses similarity between individuals' marker haplotypes to determine if QTL alleles are identical by descent (IBD) to model covariances among individuals' QTL alleles for a mixed linear model. Mapping accuracy with this method was found to be sensitive to the number of linked markers that was included in the haplotype when fitting the model at a putative position of the QTL. The objective of this study was to determine the optimal haplotype structure for this IBD-based method for fine mapping a QTL in a previously identified QTL region. Haplotypes consisting of 1, 2, 4, 6, or all 10 available markers were fit as a "sliding window" across the QTL region under ideal and nonideal simulated population conditions. It was found that using haplotypes of 4 or 6 markers as a sliding "window" resulted in the greatest mapping accuracy under nearly all conditions, although the true IBD state at a putative QTL position was most accurately predicted by IBD probabilities obtained using all markers. Using 4 or 6 markers resulted in greater discrimination of IBD probabilities between positions while maintaining sufficient accuracy of IBD probabilities to detect the QTL. Fitting IBD probabilities on the basis of a single marker resulted in the worst mapping accuracy under all conditions because it resulted in poor accuracy of IBD probabilities. In conclusion, for fine mapping using IBD methods, marker information must be used in a manner that results in sensitivity of IBD probabilities to the putative position of the QTL while maintaining sufficient accuracy of IBD probabilities to detect the QTL. Contrary to expectation, use of haplotypes of 4-6 markers to derive IBD probabilities, rather than all available markers, best fits these criteria. Thus for populations similar to those simulated here, optimal mapping accuracy for this IBD-based fine-mapping method is obtained with a haplotype structure including a subset of all available markers.
Collapse
Affiliation(s)
- L Grapes
- Department of Animal Science and Center for Integrated Animal Genomics, Iowa State University, Ames 50011, USA
| | | | | | | | | |
Collapse
|
6
|
Glenn KL, Grapes L, Suwanasopee T, Harris DL, Li Y, Wilson K, Rothschild MF. SNP analysis of AMY2 and CTSL genes in Litopenaeus vannamei and Penaeus monodon shrimp. Anim Genet 2005; 36:235-6. [PMID: 15932404 DOI: 10.1111/j.1365-2052.2005.01274.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Genetic studies in shrimp have focused on disease, with production traits such as growth left unexamined. Two shrimp species, Litopenaeus vannamei and Penaeus monodon, which represent the majority of US shrimp imports, were selected for single nucleotide polymorphism (SNP) discovery in alpha-amylase (AMY2) and cathepsin-l (CTSL), both candidate genes for growth. In L. vannamei, four SNPs were found in AMY2 and one SNP was found in CTSL. In P. monodon, one SNP was identified in CTSL. The CTSL gene was mapped to linkage group 28 of P. monodon using the female map developed with the Australian P. monodon mapping population. Association analyses for the AMY2 and CTSL genes with body weight (BW) were performed in two L. vannamei populations. While neither gene was found to be significantly associated with BW in these populations, there was a trend in one population towards higher BW for allele G of CTSL SNP C681G.
Collapse
Affiliation(s)
- K L Glenn
- Department of Animal Science and the Center for Integrated Animal Genomics, Iowa State University, Ames, IA 50011, USA
| | | | | | | | | | | | | |
Collapse
|
7
|
Gaboreanu AM, Grapes L, Ramos AM, Kim JJ, Rothschild MF. Characterization of an X-chromosome PCR-RFLP marker associated with fat deposition and growth in the pig. Anim Genet 2004; 35:401-3. [PMID: 15373745 DOI: 10.1111/j.1365-2052.2004.01178.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The X-chromosome, highly conserved within mammals, has been shown to contain major quantitative trait loci (QTL) for growth and fat deposition in the pig. We have discovered a BamHI polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) marker that was assigned to the porcine X-chromosome by two-point and multi-point linkage analysis following genotyping of a three-generation Berkshire by Yorkshire reference family. The marker was positioned 9 cM telomeric to SW2126 and 15.6 cM centromeric to SW1943. Sequence flanking the marker was found to have high similarity to existing database porcine DNA repeat elements. Association analyses of the BamHI marker for growth and meat quality traits in the reference family revealed significant association with marbling (P < 0.03), 10th rib back fat (P < 0.09) and total lipid percentage (P < 0.05), as well as with loin eye area (P < 0.04), average glycolytic potential (P < 0.03) and average lactate content (P < 0.04). Further studies are required to determine the X-chromosome functional gene affecting fat deposition and growth in the pig.
Collapse
Affiliation(s)
- A-M Gaboreanu
- Department of Animal Science, Iowa State University, Ames 50011-3150, USA
| | | | | | | | | |
Collapse
|
8
|
Abstract
Recently, a method for fine mapping quantitative trait loci (QTL) using linkage disequilibrium was proposed to map QTL by modeling covariance between individuals, due to identical-by-descent (IBD) QTL alleles, on the basis of the similarity of their marker haplotypes under an assumed population history. In the work presented here, the advantage of using marker haplotype information for fine mapping QTL was studied by comparing the IBD-based method with 10 markers to regression on a single marker, a pair of markers, or a two-locus haplotype under alternative population histories. When 10 markers were genotyped, the IBD-based method estimated the position of the QTL more accurately than did single-marker regression in all populations. When 20 markers were genotyped for regression, as single-marker methods do not require knowledge of haplotypes, the mapping accuracy of regression in all populations was similar to or greater than that of the IBD-based method using 10 markers. Thus for populations similar to those simulated here, the IBD-based method is comparable to single-marker regression analysis for fine mapping QTL.
Collapse
Affiliation(s)
- L Grapes
- Department of Animal Science, Iowa State University, Ames, Iowa 50011, USA
| | | | | | | |
Collapse
|
9
|
Affiliation(s)
- L Grapes
- Department of Animal Science, Iowa State University, Ames 50011, USA
| | | | | |
Collapse
|
10
|
Yang W, Diehl JR, Grapes L, Rothschild MF, Roudebush WE. The pig platelet-activating factor receptor gene is expressed at the mRNA level in different tissues and is mapped to chromosome 6. Anim Reprod Sci 2002; 70:277-82. [PMID: 11943497 DOI: 10.1016/s0378-4320(02)00019-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
After the pig platelet-activating factor receptor (PAFr) gene was cloned and sequenced, the chromosomal location of this gene was studied using a pig/rodent somatic cell hybrid panel containing 27 cell lines. The results indicated that the pig PAFr gene is located on SSC6q22-23. Platelet-activating factor (PAF, 1-O-alkyl-2-acetyl-sn-glycero-3-phosphocholine) is thought to be very important in the animal reproductive processes. Its function is mediated through a membrane-bound receptor. Pig PAFr mRNA distribution in different tissues was tested using reverse transcription and PCR (RT-PCR) reactions. All tissues examined expressed PAFr. Using a pig PAFr gene DNA competitor, PAFr expression was quantificated. The pig PAFr mRNA expression level was estimated to be from 1 x 10(2) to 1.2 x 10(4) copies of complementary DNA (cDNA) per 50 ng of total RNA. The highest level was found in lung, and the lowest in the skeletal muscle. These results demonstrated that PAFr was differentially expressed in pig tissues.
Collapse
Affiliation(s)
- Wensheng Yang
- Department of Animal and Veterinary Sciences, Clemson University, SC 29634, USA
| | | | | | | | | |
Collapse
|
11
|
Affiliation(s)
- L Grapes
- Department of Animal Science, Iowa State University, Ames, IA 50011-3150, USA
| | | |
Collapse
|
12
|
Grapes L, Malek M, Rothschild MF. Identification of monozygous twins and microsatellite mutation rate in pigs from QTL linkage analysis data. J Anim Breed Genet 2001. [DOI: 10.1046/j.1439-0388.2001.00295.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|