Construction of high-density linkage maps for mapping quantitative trait loci for multiple traits in field pea (Pisum sativum L.)

BMC Plant Biology

Volumn 18, Issue 1, 2018, Pages

  Gali, Krishna K ^a   Liu, Yong ^a   Sindhu, Anoop ^b   Diapari, Marwan ^c   Shunmugam, Arun S K ^d   Arganosa, Gene ^a   Daba, Ketema ^a   Caron, Carolyn ^a   Lachagari, Reddy V B ^e   Tar'an, Bunyamin ^a   Warkentin, Thomas D ^a  

^a UNIVERSITY OF SASKATCHEWAN   (Canada)

^b CHS   (United States)

^c LONDON RESEARCH AND DEVELOPMENT CENTRE   (Canada)

^d NATIONAL RESEARCH COUNCIL CANADA   (Canada)

^e AgriGenome Labs Private Limited   (India)

Author keywords

Pea; Pisum sativum L.; Quantitative trait loci

Indexed keywords

ASCOMYCETES; CHROMOSOMAL MAPPING; DISEASE RESISTANCE; GENETIC LINKAGE; GENETICS; GENOTYPE; MICROBIOLOGY; PEA; PHENOTYPE; PHYSIOLOGY; PLANT DISEASE; QUANTITATIVE TRAIT LOCUS; SINGLE NUCLEOTIDE POLYMORPHISM;

ASCOMYCOTA; CHROMOSOME MAPPING; DISEASE RESISTANCE; GENETIC LINKAGE; GENOTYPE; PEAS; PHENOTYPE; PLANT DISEASES; POLYMORPHISM, SINGLE NUCLEOTIDE; QUANTITATIVE TRAIT LOCI;

EID: 85051739634     PISSN: None     EISSN: 14712229     Source Type: Journal    
DOI: 10.1186/s12870-018-1368-4     Document Type: Article

References (50)

1. Burstin J, Gallardo K, Mir RR, Varshney RK, Duc G. Improving protein content and nutrition quality. In: Pratap A, Kumar J, editors. Biology and breeding of food legumes. Wallingford, CT: CAB International; 2011. p. 314-28.
2. Tayeh N, Aubert G, Pilet-Nayel M-L, Lejeune-Henaut I, Warkentin TD, Burstin J. Genomic tools in pea breeding programs: status and perspectives. Front Plant Sci. 2015;6:1037.
3. Warkentin TD, Smykal P, Coyne CJ, Weeden N, Domoney C, Bing D, et al. Pea (Pisum sativum L.). In: De Ron AM, editor. Grain Legumes. New York: Springer; 2015. p. 37-83.
4. Vignesh M, Shanmugavadivel PS, Kokiladevi E. Molecular markers in pea breeding - a review. Agri Reviews. 2011;32(3):183-92.
5. Smýkal P, Aubert G, Burstin J, Coyne C, Ellis N, Flavell AJ, et al. Pea (Pisum sativum L.) in the genomic era. Agronomy. 2012;2(2):74-115.
6. Lavaud C, Lesne A, Piriou C, Le Roy G, Boutet G, Moussart A, et al. Validation of QTL for resistance to Aphanomyces euteiches in different pea genetic backgrounds using near-isogenic lines. Theor Appl Genet. 2015;128(11):2273-88.
7. Ott J, Wang J, Leal SM. Genetic linkage analysis in the age of whole-genome sequencing. Nature Rev Genet. 2015;16(5):275-84.
8. Varshney RK, Terauchi R, McCouch SR. Harvesting the promising fruits of genomics: applying genome sequencing technologies to crop breeding. PLoS Biol. 2014;12(6):e1001883.
9. Zhu Y, Chen K, Mi X, Chen T, Ali J, Ye G, et al. Identification and fine mapping of a stably expressed QTL for cold tolerance at the booting stage using an interconnected breeding population in rice. PLoS One. 2015;10(12):e0145704.
10. Sindhu A, Ramsay L, Sanderson LA, Stonehouse R, Li R, Condie J, et al. Gene-based SNP discovery and genetic mapping in pea. Theor Appl Genet. 2014;127(10):2225-41.
11. Bordat A, Savois V, Nicolas M, Salse J, Chauveau A, Bourgeois M, et al. Translational genomics in legumes allowed placing in silico 5460 unigenes on the pea functional map and identified candidate genes in Pisum sativum L. G3-Genes, Genomes, Genetics (Bethesda). 2011;1(2):93-103.
12. Tayeh N, Aluome C, Falque M, Jacquin F, Klein A. Chauveau, a, et al. development of two major resources for pea genomics: the GenoPea 13.2K SNP Array and a high density, high resolution consensus genetic map. Plant J. 2015;84(6):1257-73.
13. Elshire RJ, Glaubitz JC, Sun Q, Poland JA, Kawamoto K, Buckler ES, Mitchell SE. A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS One. 2011;6(5):e19379.
14. Celik I, Gurbuz N, Uncu AT, Frary A, Doganlar S. Genome-wide SNP discovery and QTL mapping for fruit quality traits in inbred backcross lines (IBLs) of Solanum pimpinellifolium using genotyping by sequencing. BMC Genomics. 2017;18:1.
15. Lee J, Izzah NK, Choi BS, Joh HJ, Lee SC, Perumal S, et al. Genotyping-by-sequencing map permits identification of clubroot resistance QTLs and revision of the reference genome assembly in cabbage (Brassica oleracea L.). DNA Res. 2016;23(1):29-41.
16. Saxena RK, Singh VK, Kale SM, Tathineni R, Parupalli S, Kumar V, et al. Construction of genotyping-by-sequencing based high-density genetic maps and QTL mapping for fusarium wilt resistance in pigeonpea. Sci Rep. 2017;7(1):1911.
17. Jha AB, Gali KK, Tar'an B, Warkentin TD. Fine mapping of QTLs for Ascochyta blight resistance in pea using heterogeneous inbred families. Front Plant Sci. 2017;8:765.
18. Huang S, Gali KK, Tar'an B, Warkentin TD, Bueckert RA. 2017. Pea phenology: crop potential in a warming environment. Crop Sci. 2017;57(3):1540-51.
19. Boutet G, Carvalho SA, Falque M, Peterlongo P, Lhuillier E, Bouchez O, et al. SNP discovery and genetic mapping using genotyping by sequencing of whole genome genomic DNA from a pea RIL population. BMC Genomics. 2016;17:121.
20. Morrell PL, Buckler ES, Ross-Ibarra J. Crop genomics: advances and applications. Nat Rev Genet. 2012;13(2):85-96.
21. Verhoeven KJF, Casella G, McIntyre LM. Epistasis: obstacle or advantage for mapping complex traits? PLoS One. 2010;5(8):e12264.
22. Tar'an B, Warkentin T, Somers DJ, Miranda D, Vandenberg A, Blade S, et al. Quantitative trait loci for lodging resistance, plant height and partial resistance to Mycosphaerella blight in field pea (Pisum sativum L.). Theor. Appl. Genet. 2003;107(8):1482-91.
23. Warkentin T, Vandenberg A, Banniza S, Slinkard A. CDC Striker field plea. Can J Plant Sci. 2004;84(1):239-40.
24. Warkentin T, Vandenberg A, Tar'an B, Banniza S, Barlow B, Ife S. CDC meadow field pea. Can J Plant Sci. 2007;87(4):909-10.
25. Warkentin TD, Delgerjav O, Arganosa G, Rehman AU, Bett KE, Anbessa Y, et al. Development and characterization of low-phytate pea. Crop Sci. 2012;52(1):74-8.
26. Kosambi DD. The estimation of map distances from recombination values. Ann Eugenics. 1943;12:172-5.
27. Wu Y, Bhat PR, Close TJ, Lonardi S. Efficient and accurate construction of genetic linkage maps from the minimum spanning tree of a graph. PLoS Genet. 2008;4(10):e1000212.
28. Diapari M, Sindhu A, Warkentin TD, Bett KE, Ramsay L, Sharpe AG, Tar'an B. Population structure and marker-trait association studies of iron, zinc and selenium concentration in seed of field pea (Pisum sativum L.). Mol Breeding. 2015;35:30. https://doi.org/10.1007/s11032-015-0252-2.
29. Arganosa GC, Warkentin TD, Racz VJ, Blade S, Hsu H, Philips C. Prediction of crude protein content in field peas grown in Saskatchewan using near infrared reflectance spectroscopy. Can J Plant Sci. 2006;86:157-9.
30. Jha AB, Tar'an B, Stonehouse R, Warkentin TD. Identification of QTLs associated with improved resistance to Ascochyta blight in an interspecific pea recombinant inbred line population. Crop Sci. 2016;56:2926-39.
31. Ubayasena K, Bett K, Tar'an B, Warkentin TD. Genetic control and identification of QTLs associated with visual quality traits of field pea (Pisum sativum L.). Genome. 2011;54:261-72.
32. Shapiro SS, Wilk MB. An analysis of variance test for normality (complete samples). Biometrika. 1965;52:591-611.
33. Wang S, Basten CJ, Zeng ZB: Windows QTL Cartographer 2.5. http://statgen.ncsu.edu/qtlcart/WQTLCart.htm (2007). Accessed 23 Mar 2018.
34. Gawalko E, Garrett RG, Warkentin TD, Wang N, Richter A. Trace elements in Canadian peas: a grain safety assurance perspective. Food Addit Contam. 2009;26:1002-12.
35. Yang Z, Chen Z, Peng Z, Yu Y, Liao M, Wei S. Development of a high-density linkage map and mapping of the three-pistil gene (Pis1) in wheat using GBS markers. BMC Genomics. 2017;18:567.
36. Ma Y, Coyne CJ, Grusak MA, Mazourek M, Cheng P, Main D, RJ MG. Genome-wide SNP identification, linkage map construction and QTL mapping for seed mineral concentrations and contents in pea (Pisum sativum L.). BMC Plant Biol. 2017;17:43.
37. Liu H, Bayer M, Druka A, Ressell JR, Hackett CA, Poland J, et al. An evaluation of genotyping by sequencing (GBS) to map the Breviaristatum-e (ari-e) locus in cultivated barley. BMC Genomics. 2014;15:104.
38. Weller JL, Liew LC, Hecht VF, Rajandran V, Laurie RE, Ridge S, et al. A conserved molecular basis for photoperiod adaptation in two temperate legumes. PNAS. 2012;109(51):21158-63.
39. Henaut L, Hanocq E, Bethencourt L, Fontaine V, Delbreil B, Morin J, et al. The flowering locus Hr colocalizes with a major QTL affecting winter frost tolerance in Pisum sativum L. Theor. Appl. Genet. 2008;116(8):1105-16.
40. Vanhala T, Normann KR, Lundstrom M, Weller JL, Leino MW, Hagenblad J. Flowering time adaption in Swedish landrace pea (Pisum sativum L.). BMC Genet. 2016;17:117.
41. Hamon C, Coyne CJ, McGee RJ, Lesne A. QTL meta-analysis provides a comprehensive view of loci controlling partial resistance to Aphanomycces euteiches in four sources of resistance in pea. BMC Plant Biol. 2013;13:45.
42. Kujur A, Upadhyaya HD, Bajaj D, Gowda CL, Sharma S, Tyagi AK, Parida SK. Identification of candidate genes and natural allelic variants for QTLs governing plant height in chickpea. Sci Rep. 2016;6:27968.
43. Smitchger, J.A. Quantitative trait loci associated with lodging, stem strength, yield, and other important agronomic traits in dry field peas. https://zenodo.org/record/840399#.Wizg-k1hiM8 (2017). Accessed 09 Dec 2017.
44. Wang TF, Gossen BD, Slinkard AE. Lodging increases severity and impact of Mycosphaerella blight on field pea. Can J Plant Sci. 2006;86(3):855-63.
45. Fondevilla S, Almeida NF, Satovic Z, Rubiales D, Patto MCV, Cubero JI, Torres AM. Identification of common genomic regions controlling resistance to Mycosphaerella pinodes, earliness and architectural traits in different pea genetic backgrounds. Euphytica. 2011;182(1):43-52.
46. Prioul-Gervais S, Deniot G, Receveur EM, Frankewitz A, Fourmann M, Rameau C, et al. Candidate genes for quantitative resistance to Ascochyta pinodes in pea (Pisum sativum L.). Theor. Appl. Genet. 2007;114(6):971-84.
47. Tar'an B, Warkentin T, Somers DJ, Miranda D, Vandenberg A, Blade S, Bing D. Identification of quantitative trait loci for grain yield, seed protein concentration and maturity in field pea (Pisum sativum L.). Euphytica. 2004;136(3):297-306.
48. Krajewski P, Bocianowski J, Gawlowska M, Kaczmarek Z, Pniewski T, Swiecicki W, Wolko B. QTL for yield components and protein content: a multienvironment study of two pea (Pisum sativum L.) populations. Euphytica. 2012;183(3):323-36.
49. Annicchiarico P, Nazziacari N, Pecetti L, Romani M, Ferrari B, Wei Y, Brummer EC. GBS-based genomic selection for pea grain yield under severe terminal drought. Plant Genome. 2017;10(2) https://doi.org/10.3835/plantgenome2016.07.0072.
50. Shunmugam ASK, Liu X, Stonehouse R, Tar'an B, Bett KE, Sharpe AG, Warkentin TD. Mapping seed phytic acid concentration and iron bioavailability in a pea recombinant inbred line population. Crop Sci. 2015;55(2):828-36.