1
|
N’Diaye A, Haile JK, Fowler DB, Ammar K, Pozniak CJ. Effect of Co-segregating Markers on High-Density Genetic Maps and Prediction of Map Expansion Using Machine Learning Algorithms. FRONTIERS IN PLANT SCIENCE 2017; 8:1434. [PMID: 28878789 PMCID: PMC5572363 DOI: 10.3389/fpls.2017.01434] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 08/03/2017] [Indexed: 05/28/2023]
Abstract
Advances in sequencing and genotyping methods have enable cost-effective production of high throughput single nucleotide polymorphism (SNP) markers, making them the choice for linkage mapping. As a result, many laboratories have developed high-throughput SNP assays and built high-density genetic maps. However, the number of markers may, by orders of magnitude, exceed the resolution of recombination for a given population size so that only a minority of markers can accurately be ordered. Another issue attached to the so-called 'large p, small n' problem is that high-density genetic maps inevitably result in many markers clustering at the same position (co-segregating markers). While there are a number of related papers, none have addressed the impact of co-segregating markers on genetic maps. In the present study, we investigated the effects of co-segregating markers on high-density genetic map length and marker order using empirical data from two populations of wheat, Mohawk × Cocorit (durum wheat) and Norstar × Cappelle Desprez (bread wheat). The maps of both populations consisted of 85% co-segregating markers. Our study clearly showed that excess of co-segregating markers can lead to map expansion, but has little effect on markers order. To estimate the inflation factor (IF), we generated a total of 24,473 linkage maps (8,203 maps for Mohawk × Cocorit and 16,270 maps for Norstar × Cappelle Desprez). Using seven machine learning algorithms, we were able to predict with an accuracy of 0.7 the map expansion due to the proportion of co-segregating markers. For example in Mohawk × Cocorit, with 10 and 80% co-segregating markers the length of the map inflated by 4.5 and 16.6%, respectively. Similarly, the map of Norstar × Cappelle Desprez expanded by 3.8 and 11.7% with 10 and 80% co-segregating markers. With the increasing number of markers on SNP-chips, the proportion of co-segregating markers in high-density maps will continue to increase making map expansion unavoidable. Therefore, we suggest developers improve linkage mapping algorithms for efficient analysis of high-throughput data. This study outlines a practical strategy to estimate the IF due to the proportion of co-segregating markers and outlines a method to scale the length of the map accordingly.
Collapse
Affiliation(s)
- Amidou N’Diaye
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, SaskatoonSK, Canada
| | - Jemanesh K. Haile
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, SaskatoonSK, Canada
| | - D. Brian Fowler
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, SaskatoonSK, Canada
| | - Karim Ammar
- International Maize and Wheat Improvement Center (CIMMYT)Texcoco, Mexico
| | - Curtis J. Pozniak
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, SaskatoonSK, Canada
| |
Collapse
|
2
|
Vontimitta V, Olukolu BA, Penning BW, Johal G, Balint-Kurti PJ. The genetic basis of flecking and its relationship to disease resistance in the IBM maize mapping population. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015; 128:2331-9. [PMID: 26239408 DOI: 10.1007/s00122-015-2588-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2014] [Accepted: 07/16/2015] [Indexed: 05/20/2023]
Abstract
In this paper, we determine the genetic architecture controlling leaf flecking in maize and investigate its relationship to disease resistance and the defense response. Flecking is defined as a mild, often environmentally dependent lesion phenotype observed on the leaves of several commonly used maize inbred lines. Anecdotal evidence suggests a link between flecking and enhanced broad-spectrum disease resistance. Neither the genetic basis underlying flecking nor its possible relationship to disease resistance has been systematically evaluated. The commonly used maize inbred Mo17 has a mild flecking phenotype. The IBM-advanced intercross mapping population, derived from a cross between Mo17 and another commonly used inbred B73, has been used for mapping a number of traits in maize including several related to disease resistance. In this study, flecking was assessed in the IBM population over 6 environments. Several quantitative trait loci for flecking were identified, with the strongest one located on chromosome 6. Low but moderately significant correlations were observed between stronger flecking and higher disease resistance with respect to two diseases, southern leaf blight and northern leaf blight and between stronger flecking and a stronger defense response.
Collapse
Affiliation(s)
- Vijay Vontimitta
- Botany and Plant Pathology, Purdue University, Lilly Hall, West Lafayette, IN, 47907-2054, USA
| | - Bode A Olukolu
- Department of Plant Pathology, NC State University, 2574 Thomas Hall, Raleigh, NC, 27695-7616, USA
- Department of Crop Science, NC State University, Raleigh, NC, 27695-7620, USA
| | - Bryan W Penning
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Gurmukh Johal
- Botany and Plant Pathology, Purdue University, Lilly Hall, West Lafayette, IN, 47907-2054, USA
| | - P J Balint-Kurti
- Department of Plant Pathology, NC State University, 2574 Thomas Hall, Raleigh, NC, 27695-7616, USA.
- USDA-ARS Plant Science Research Unit, Raleigh, NC, 27695, USA.
| |
Collapse
|
3
|
Šimić D, Lepeduš H, Jurković V, Antunović J, Cesar V. Quantitative genetic analysis of chlorophyll a fluorescence parameters in maize in the field environments. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2014; 56:695-708. [PMID: 24521148 DOI: 10.1111/jipb.12179] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 02/11/2014] [Indexed: 06/03/2023]
Abstract
Chlorophyll fluorescence transient from initial to maximum fluorescence ("P" step) throughout two intermediate steps ("J" and "I") (JIP-test) is considered a reliable early quantitative indicator of stress in plants. The JIP-test is particularly useful for crop plants when applied in variable field environments. The aim of the present study was to conduct a quantitative trait loci (QTL) analysis for nine JIP-test parameters in maize during flowering in four field environments differing in weather conditions. QTL analysis and identification of putative candidate genes might help to explain the genetic relationship between photosynthesis and different field scenarios in maize plants. The JIP-test parameters were analyzed in the intermated B73 × Mo17 (IBM) maize population of 205 recombinant inbred lines. A set of 2,178 molecular markers across the whole maize genome was used for QTL analysis revealing 10 significant QTLs for seven JIP-test parameters, of which five were co-localized when combined over the four environments indicating polygenic inheritance and pleiotropy. Our results demonstrate that QTL analysis of chlorophyll fluorescence parameters was capable of detecting one pleiotropic locus on chromosome 7, coinciding with the gene gst23 that may be associated with efficient photosynthesis under different field scenarios.
Collapse
Affiliation(s)
- Domagoj Šimić
- Agricultural Institute Osijek, HR-31103, Osijek, Croatia
| | | | | | | | | |
Collapse
|
4
|
Ganal MW, Durstewitz G, Polley A, Bérard A, Buckler ES, Charcosset A, Clarke JD, Graner EM, Hansen M, Joets J, Le Paslier MC, McMullen MD, Montalent P, Rose M, Schön CC, Sun Q, Walter H, Martin OC, Falque M. A large maize (Zea mays L.) SNP genotyping array: development and germplasm genotyping, and genetic mapping to compare with the B73 reference genome. PLoS One 2011; 6:e28334. [PMID: 22174790 PMCID: PMC3234264 DOI: 10.1371/journal.pone.0028334] [Citation(s) in RCA: 378] [Impact Index Per Article: 29.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2011] [Accepted: 11/05/2011] [Indexed: 01/05/2023] Open
Abstract
SNP genotyping arrays have been useful for many applications that require a large number of molecular markers such as high-density genetic mapping, genome-wide association studies (GWAS), and genomic selection. We report the establishment of a large maize SNP array and its use for diversity analysis and high density linkage mapping. The markers, taken from more than 800,000 SNPs, were selected to be preferentially located in genes and evenly distributed across the genome. The array was tested with a set of maize germplasm including North American and European inbred lines, parent/F1 combinations, and distantly related teosinte material. A total of 49,585 markers, including 33,417 within 17,520 different genes and 16,168 outside genes, were of good quality for genotyping, with an average failure rate of 4% and rates up to 8% in specific germplasm. To demonstrate this array's use in genetic mapping and for the independent validation of the B73 sequence assembly, two intermated maize recombinant inbred line populations - IBM (B73×Mo17) and LHRF (F2×F252) - were genotyped to establish two high density linkage maps with 20,913 and 14,524 markers respectively. 172 mapped markers were absent in the current B73 assembly and their placement can be used for future improvements of the B73 reference sequence. Colinearity of the genetic and physical maps was mostly conserved with some exceptions that suggest errors in the B73 assembly. Five major regions containing non-colinearities were identified on chromosomes 2, 3, 6, 7 and 9, and are supported by both independent genetic maps. Four additional non-colinear regions were found on the LHRF map only; they may be due to a lower density of IBM markers in those regions or to true structural rearrangements between lines. Given the array's high quality, it will be a valuable resource for maize genetics and many aspects of maize breeding.
Collapse
Affiliation(s)
| | | | | | - Aurélie Bérard
- Etude du Polymorphisme des Génomes Végétaux, INRA – CEA – Institut de Génomique – Centre National de Génotypage, Evry, France
| | | | - Alain Charcosset
- UMR de Génétique Végétale, INRA – Université Paris-Sud – CNRS – AgroParisTech, Gif-sur-Yvette, France
| | - Joseph D. Clarke
- Syngenta Biotechnology Inc., Research Triangle Park, North Carolina, United States of America
| | | | - Mark Hansen
- Illumina Inc., San Diego, California, United States of America
| | - Johann Joets
- UMR de Génétique Végétale, INRA – Université Paris-Sud – CNRS – AgroParisTech, Gif-sur-Yvette, France
| | - Marie-Christine Le Paslier
- Etude du Polymorphisme des Génomes Végétaux, INRA – CEA – Institut de Génomique – Centre National de Génotypage, Evry, France
| | - Michael D. McMullen
- Plant Genetics Research Unit, USDA-Agricultural Research Service, Columbia, Missouri, United States of America
| | - Pierre Montalent
- UMR de Génétique Végétale, INRA – Université Paris-Sud – CNRS – AgroParisTech, Gif-sur-Yvette, France
| | - Mark Rose
- Syngenta Biotechnology Inc., Research Triangle Park, North Carolina, United States of America
| | - Chris-Carolin Schön
- Department of Plant Breeding, Technische Universität München, Freising, Germany
| | - Qi Sun
- Cornell University, Ithaca, New York, United States of America
| | - Hildrun Walter
- Department of Plant Breeding, Technische Universität München, Freising, Germany
| | - Olivier C. Martin
- UMR de Génétique Végétale, INRA – Université Paris-Sud – CNRS – AgroParisTech, Gif-sur-Yvette, France
| | - Matthieu Falque
- UMR de Génétique Végétale, INRA – Université Paris-Sud – CNRS – AgroParisTech, Gif-sur-Yvette, France
- * E-mail:
| |
Collapse
|
5
|
Nelson JC. Linkage analysis in unconventional mating designs in line crosses. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2011; 123:897-906. [PMID: 21681487 DOI: 10.1007/s00122-011-1635-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2011] [Accepted: 06/03/2011] [Indexed: 05/30/2023]
Abstract
Linkage estimation and genetic map construction with genotyped DNA markers in plants preferentially employ a few maximally informative early-generation or recombinant-inbred mating designs. Fitting their recombination models to unconventional designs adapted to cultivar development (series of backcrossing, selfing, haploid-doubling, random-intercrossing, and sib-mating steps) distorts single- and multipoint linkage estimates even with dense marker coverage. Two methods are provided for correct linkage estimation in unconventional designs: fitting a correct multigeneration model, or correcting the estimates produced by fitting a one-generation model with any conventional software. These methods also support calculation of multilocus genotype frequencies and QTL-genotype distributions and are available in software.
Collapse
Affiliation(s)
- James C Nelson
- Department of Plant Pathology, 4024 Throckmorton Plant Sciences Center, Kansas State University, Manhattan, KS 66506, USA.
| |
Collapse
|
6
|
The genetic architecture of grain yield and related traits in Zea maize L. revealed by comparing intermated and conventional populations. Genetics 2010; 186:395-404. [PMID: 20592258 DOI: 10.1534/genetics.110.113878] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Using advanced intermated populations has been proposed as a way to increase the accuracy of mapping experiments. An F(3) population of 300 lines and an advanced intermated F(3) population of 322 lines, both derived from the same parental maize inbred lines, were jointly evaluated for dry grain yield (DGY), grain moisture (GM), and silking date (SD). Genetic variance for dry grain yield was significantly lower in the intermated population compared to the F(3) population. The confidence interval around a QTL was on average 2.31 times smaller in the intermated population compared to the F(3) population. One controversy surrounding QTL mapping is whether QTL identified in fact represent single loci. This study identifies two distinct loci for dry grain yield in the intermated population in coupling phase, while the F(3) identifies only a single locus. Surprisingly, fewer QTL were detected in the intermated population than the F(3) (21 vs. 30) and <50% of the detected QTL were shared among the two populations. Cross-validation showed that selection bias was more important in the intermated population than in the F(3) and that each detected QTL explained a lower percentage of the variance. This finding supports the hypothesis that QTL detected in conventional populations correspond mainly to clusters of linked QTL. The actual number of QTL involved in the genetic architecture of complex traits may be substantially larger, with effect sizes substantially smaller than in conventional populations.
Collapse
|
7
|
Olukolu BA, Trainin T, Fan S, Kole C, Bielenberg DG, Reighard GL, Abbott AG, Holland D. Genetic linkage mapping for molecular dissection of chilling requirement and budbreak in apricot (Prunus armeniaca L.). Genome 2010; 52:819-28. [PMID: 19935906 DOI: 10.1139/g09-050] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Commercial production of apricot is severely affected by sensitivity to climatic conditions, an adaptive feature essential for cycling between vegetative or floral growth and dormancy. Yield losses are due to late winter or early spring frosts and inhibited vegetative or floral growth caused by unfulfilled chilling requirement (CR). Two apricot cultivars, Perfection and A.1740, were selected for high and low CR, respectively, to develop a mapping population of F1 individuals using a two-way pseudo-testcross mapping strategy. High-density male and female maps were constructed using, respectively, 655 and 592 markers (SSR and AFLP) spanning 550.6 and 454.9 cM with average marker intervals of 0.84 and 0.77 cM. CR was evaluated in two seasons on potted trees forced to break buds after cold treatments ranging from 100 to 900 h. A total of 12 putative CR quantitative trait loci (QTLs) were detected on six linkage groups using composite interval mapping and a simultaneous multiple regression fit. QTL main effects of additive and additive x additive interactions accounted for 58.5% +/- 6.7% and 66.1% +/- 5.8% of the total phenotypic variance in the Perfection and A.1740 maps, respectively. We report two apricot high-density maps and QTLs corresponding to map positions of differentially expressed transcripts and suggested candidate genes controlling CR.
Collapse
Affiliation(s)
- Bode A Olukolu
- Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA
| | | | | | | | | | | | | | | |
Collapse
|
8
|
Capelle V, Remoué C, Moreau L, Reyss A, Mahé A, Massonneau A, Falque M, Charcosset A, Thévenot C, Rogowsky P, Coursol S, Prioul JL. QTLs and candidate genes for desiccation and abscisic acid content in maize kernels. BMC PLANT BIOLOGY 2010; 10:2. [PMID: 20047666 PMCID: PMC2826337 DOI: 10.1186/1471-2229-10-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2009] [Accepted: 01/04/2010] [Indexed: 05/17/2023]
Abstract
BACKGROUND Kernel moisture at harvest is an important trait since a low value is required to prevent unexpected early germination and ensure seed preservation. It is also well known that early germination occurs in viviparous mutants, which are impaired in abscisic acid (ABA) biosynthesis. To provide some insight into the genetic determinism of kernel desiccation in maize, quantitative trait loci (QTLs) were detected for traits related to kernel moisture and ABA content in both embryo and endosperm during kernel desiccation. In parallel, the expression and mapping of genes involved in kernel desiccation and ABA biosynthesis, were examined to detect candidate genes. RESULTS The use of an intermated recombinant inbred line population allowed for precise QTL mapping. For 29 traits examined in an unreplicated time course trial of days after pollination, a total of 78 QTLs were detected, 43 being related to kernel desiccation, 15 to kernel weight and 20 to ABA content. Multi QTL models explained 35 to 50% of the phenotypic variation for traits related to water status, indicating a large genetic control amenable to breeding. Ten of the 20 loci controlling ABA content colocated with previously detected QTLs controlling water status and ABA content in water stressed leaves. Mapping of candidate genes associated with kernel desiccation and ABA biosynthesis revealed several colocations between genes with putative functions and QTLs. Parallel investigation via RT-PCR experiments showed that the expression patterns of the ABA-responsive Rab17 and Rab28 genes as well as the late embryogenesis abundant Emb5 and aquaporin genes were related to desiccation rate and parental allele effect. Database searches led to the identification and mapping of two zeaxanthin epoxidase (ZEP) and five novel 9-cis-epoxycarotenoid dioxygenase (NCED) related genes, both gene families being involved in ABA biosynthesis. The expression of these genes appeared independent in the embryo and endosperm and not correlated with ABA content in either tissue. CONCLUSIONS A high resolution QTL map for kernel desiccation and ABA content in embryo and endosperm showed several precise colocations between desiccation and ABA traits. Five new members of the maize NCED gene family and another maize ZEP gene were identified and mapped. Among all the identified candidates, aquaporins and members of the Responsive to ABA gene family appeared better candidates than NCEDs and ZEPs.
Collapse
Affiliation(s)
- Valérie Capelle
- Univ Paris-Sud, Institut de Biotechnologie des Plantes, Bât 630, F-91405 Orsay, France
- CNRS, UMR 8618, F-91405 Orsay, France
| | - Carine Remoué
- CNRS, UMR 8618, F-91405 Orsay, France
- CNRS, UMR 0320/UMR 8120 Génétique Végétale, F-91190 Gif-sur-Yvette, France
| | - Laurence Moreau
- INRA, UMR 0320/UMR 8120 Génétique Végétale, F-91190 Gif-sur-Yvette, France
| | - Agnès Reyss
- Univ Paris-Sud, Institut de Biotechnologie des Plantes, Bât 630, F-91405 Orsay, France
- CNRS, UMR 8618, F-91405 Orsay, France
| | - Aline Mahé
- Univ Paris-Sud, Institut de Biotechnologie des Plantes, Bât 630, F-91405 Orsay, France
- CNRS, UMR 8618, F-91405 Orsay, France
| | - Agnès Massonneau
- INRA, Reproduction et Développement des Plantes, UMR 879 INRA-CNRS-ENSL-UCBL, IFR128 Biosciences Lyon-Gerland, F-69364 Lyon Cedex 07, France
- 52, Av de la Marjolaine, 34110 Frontigan, France
| | - Matthieu Falque
- INRA, UMR 0320/UMR 8120 Génétique Végétale, F-91190 Gif-sur-Yvette, France
| | - Alain Charcosset
- INRA, UMR 0320/UMR 8120 Génétique Végétale, F-91190 Gif-sur-Yvette, France
| | - Claudine Thévenot
- Univ Paris-Sud, Institut de Biotechnologie des Plantes, Bât 630, F-91405 Orsay, France
- CNRS, UMR 8618, F-91405 Orsay, France
| | - Peter Rogowsky
- INRA, Reproduction et Développement des Plantes, UMR 879 INRA-CNRS-ENSL-UCBL, IFR128 Biosciences Lyon-Gerland, F-69364 Lyon Cedex 07, France
| | - Sylvie Coursol
- INRA, UMR 0320/UMR 8120 Génétique Végétale, F-91190 Gif-sur-Yvette, France
| | - Jean-Louis Prioul
- Univ Paris-Sud, Institut de Biotechnologie des Plantes, Bât 630, F-91405 Orsay, France
- CNRS, UMR 8618, F-91405 Orsay, France
| |
Collapse
|
9
|
Zwonitzer JC, Bubeck DM, Bhattramakki D, Goodman MM, Arellano C, Balint-Kurti PJ. Use of selection with recurrent backcrossing and QTL mapping to identify loci contributing to southern leaf blight resistance in a highly resistant maize line. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2009; 118:911-925. [PMID: 19130030 DOI: 10.1007/s00122-008-0949-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2008] [Accepted: 12/04/2008] [Indexed: 05/27/2023]
Abstract
B73 is a historically important maize line with excellent yield potential but high susceptibility to the foliar disease southern leaf blight (SLB). NC292 and NC330 are B73 near-isogenic lines (NILs) that are highly resistant to SLB. They were derived by repeated backcrossing of an elite source of SLB resistance (NC250P) to B73, with selection for SLB resistance among and within backcross families. The goal of this paper was to characterize the loci responsible for the increased SLB resistance of NC292 and NC330 and to determine how many of the SLB disease resistance quantitative trait loci (dQTL) were selected for in the development of NC292 and NC330. Genomic regions that differentiated NC292 and NC330 from B73 and which may contribute to NC292 and NC330s enhanced SLB resistance were identified. Ten NC250P-derived introgressions were identified in both the NC292 and NC330 genomes of which eight were shared between genomes. dQTL were mapped in two F(2:3) populations derived from lines very closely related to the original parents of NC292 and NC330--(B73rhm1 x NC250A and NC250A x B73). Nine SLB dQTL were mapped in the combined populations using combined SLB disease data over all locations (SLB AllLocs). Of these, four dQTL precisely colocalized with NC250P introgressions in bins 2.05-2.06, 3.03, 6.01, and 9.02 and three were identified near NC250P introgressions in bins 1.09, 5.05-5.06, and 10.03. Therefore the breeding program used to develop NC292 and NC330 was highly effective in selecting for multiple SLB resistance alleles.
Collapse
Affiliation(s)
- John C Zwonitzer
- Department of Plant Pathology, North Carolina State University, Raleigh, NC 27695-7616, USA
| | | | | | | | | | | |
Collapse
|
10
|
Balint-Kurti PJ, Zwonitzer JC, Wisser RJ, Carson ML, Oropeza-Rosas MA, Holland JB, Szalma SJ. Precise mapping of quantitative trait loci for resistance to southern leaf blight, caused by Cochliobolus heterostrophus race O, and flowering time using advanced intercross maize lines. Genetics 2007; 176:645-57. [PMID: 17339203 PMCID: PMC1893051 DOI: 10.1534/genetics.106.067892] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2006] [Accepted: 02/21/2007] [Indexed: 11/18/2022] Open
Abstract
The intermated B73 x Mo17 (IBM) population, an advanced intercross recombinant inbred line population derived from a cross between the maize lines B73 (susceptible) and Mo17 (resistant), was evaluated in four environments for resistance to southern leaf blight (SLB) disease caused by Cochliobolus heterostrophus race O. Two environments were artificially inoculated, while two were not inoculated and consequently had substantially lower disease pressure. Four common SLB resistance quantitative trait loci (QTL) were identified in all environments, two in bin 3.04 and one each in bins 1.10 and 8.02/3. There was no significant correlation between disease resistance and days to anthesis. A direct comparison was made between SLB QTL detected in two populations, independently derived from the same parental cross: the IBM advanced intercross population and a conventional recombinant inbred line population. Several QTL for SLB resistance were detected in both populations, with the IBM providing between 5 and, in one case, 50 times greater mapping resolution.
Collapse
Affiliation(s)
- P J Balint-Kurti
- Department of Plant Pathology, North Carolina State University, Raleigh, North Carolina 27695-7616, USA.
| | | | | | | | | | | | | |
Collapse
|
11
|
Fu Y, Wen TJ, Ronin YI, Chen HD, Guo L, Mester DI, Yang Y, Lee M, Korol AB, Ashlock DA, Schnable PS. Genetic dissection of intermated recombinant inbred lines using a new genetic map of maize. Genetics 2006; 174:1671-83. [PMID: 16951074 PMCID: PMC1667089 DOI: 10.1534/genetics.106.060376] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A new genetic map of maize, ISU-IBM Map4, that integrates 2029 existing markers with 1329 new indel polymorphism (IDP) markers has been developed using intermated recombinant inbred lines (IRILs) from the intermated B73xMo17 (IBM) population. The website http://magi.plantgenomics.iastate.edu provides access to IDP primer sequences, sequences from which IDP primers were designed, optimized marker-specific PCR conditions, and polymorphism data for all IDP markers. This new gene-based genetic map will facilitate a wide variety of genetic and genomic research projects, including map-based genome sequencing and gene cloning. The mosaic structures of the genomes of 91 IRILs, an important resource for identifying and mapping QTL and eQTL, were defined. Analyses of segregation data associated with markers genotyped in three B73/Mo17-derived mapping populations (F2, Syn5, and IBM) demonstrate that allele frequencies were significantly altered during the development of the IBM IRILs. The observations that two segregation distortion regions overlap with maize flowering-time QTL suggest that the altered allele frequencies were a consequence of inadvertent selection. Detection of two-locus gamete disequilibrium provides another means to extract functional genomic data from well-characterized plant RILs.
Collapse
Affiliation(s)
- Yan Fu
- Interdepartmental Genetics Graduate Program, Iowa State University, Ames, Iowa 50011-3467, USA
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
12
|
Falque M, Décousset L, Dervins D, Jacob AM, Joets J, Martinant JP, Raffoux X, Ribière N, Ridel C, Samson D, Charcosset A, Murigneux A. Linkage mapping of 1454 new maize candidate gene Loci. Genetics 2005; 170:1957-66. [PMID: 15937132 PMCID: PMC1449757 DOI: 10.1534/genetics.104.040204] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2004] [Accepted: 04/24/2005] [Indexed: 11/18/2022] Open
Abstract
Bioinformatic analyses of maize EST sequences have highlighted large numbers of candidate genes putatively involved in agriculturally important traits. To contribute to ongoing efforts toward mapping of these genes, we used two populations of intermated recombinant inbred lines (IRILs), which allow a higher map resolution than nonintermated RILs. The first panel (IBM), derived from B73 x Mo17, is publicly available from the Maize Genetics Cooperation Stock Center. The second panel (LHRF) was developed from F2 x F252 to map loci monomorphic on IBM. We built framework maps of 237 loci from the IBM panel and 271 loci from the LHRF panel. Both maps were used to place 1454 loci (1056 on map IBM_Gnp2004 and 398 on map LHRF_Gnp2004) that corresponded to 954 cDNA probes previously unmapped. RFLP was mostly used, but PCR-based methods were also performed for some cDNAs to map SNPs. Unlike in usual IRIL-based maps published so far, corrected meiotic centimorgan distances were calculated, taking into account the number of intermating generations undergone by the IRILs. The corrected sizes of our framework maps were 1825 cM for IBM_Gnp2004 and 1862 cM for LHRF_Gnp2004. All loci mapped on LHRF_Gnp2004 were also projected on a consensus map IBMconsensus_Gnp2004. cDNA loci formed clusters near the centromeres except for chromosomes 1 and 8.
Collapse
Affiliation(s)
- Matthieu Falque
- INRA-UPS-CNRS-INA.PG, UMR de Génétique Végétale, 91190 Gif-sur-Yvette, France.
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|