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Statistical and Quantitative Genetics Studies

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Genomics Data Analysis for Crop Improvement

Abstract

Quantitative genetics and plant breeding are non-exclusive and these disciplines has been benefited from each other for the past 100 years. As a matter of fact, the majority of economically significant traits in crops and livestock species are quantitative in nature rather than qualitative. Several biometricians have made a significant contribution to understand how quantitative genetics works. Different methods of plant breeding had evolved, and are still evolving. Traditional plant breeding methods emphasize the components of quantitative variance but accuracy, time, and effectiveness are the three key factors that conventional breeding faces while trying to decode this. High throughput next-generation sequencing has made it easier, more accurate, and more exact to understand the genetics of complex traits in a shorter time, which has also shortened the breeding cycles required for desired genetic gain. This book chapter mostly focused on the statistical tools that plant breeders used in their research to dissect the genetics of complex traits that are significant economically including both traditional and advance plant breeding methods.

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References

  1. Haas M, Schreiber M, Mascher M (2019) Domestication and crop evolution of wheat and barley: genes, genomics, and future directions. J Integr Plant Biol 61(3):204–225

    Article  PubMed  Google Scholar 

  2. Galton F (1889) Natural Inheritance Macmillan & Co

    Google Scholar 

  3. Pearson K (1894) Contributions to the mathematical theory of evolution. Philos Trans R Soc London A 185:71–110

    Article  Google Scholar 

  4. Bateson W, Punnett RC (1905) 1908. Experimental studies in the physiology of heredity. In: Peters JA (ed) Classic papers in genetics. Prentice-Hall, Englewood Cliffs, NJ, pp 42–59

    Google Scholar 

  5. Yule, G. U. (1906). On the theory of inheritance of quantitative compound characters on the basis of Mendel’s laws-a preliminary note. In: Rep 3rd Int. Conf Genetics, pp 140, 142

    Google Scholar 

  6. Johannsen W (1903) Ueber Erblichkeit in Populationen und in reinen Linien: ein Beitrag zur Beleuchtung schwebender Selektionsfragen. G. Fischer

    Google Scholar 

  7. Nilsson-Ehle H (1909) Kreuzungsuntersuchungen an hafer und weizen, vol 5(2). H. Ohlssonsbuchdruckerei

    Google Scholar 

  8. East EM (1916) Studies on size inheritance in Nicotiana. Genetics 1(2):164–176

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Fisher RA (1919) XV.—The correlation between relatives on the supposition of Mendelian inheritance. Earth Environ Sci Trans R Soc Edinb 52(2):399–433

    Article  Google Scholar 

  10. Wright S (1921) Systems of mating. I. The biometric relations between parent and offspring. Genetics 6(2):111–123

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Haldane JBS (1924) A mathematical theory of natural and artificial selection. Part II the influence of partial self-fertilisation, inbreeding, assortative mating, and selective fertilisation on the composition of mendelian populations, and on natural selection. Biol Rev 1(3):158–163

    Article  Google Scholar 

  12. Lush JL (1940) Intra-sire correlations or regressions of offspring on dam as a method of estimating heritability of characteristics. J Anim Sci 1940(1):293–301

    Google Scholar 

  13. Mahalanobis PC (1928) Statistical study of the Chinese head. Proceedings of the Indian science congress (Calcutta)

    Google Scholar 

  14. Sprague GF, Tatum LA (1942) General vs. specific combining ability in single crosses of corn. J Am Soc Agron 34:923–932

    Article  Google Scholar 

  15. Malécot G (1948) Les Mathématiques de l’Hérédité. Masson, Paris. (translated as The Mathematics of Heredity)

    Google Scholar 

  16. Mather K (1949) Biometrical genetics. Methuen and Co. Ltd., London, p 162

    Google Scholar 

  17. Comstock RE, Robinson HF (1948) The components of genetic variance in populations of biparental progenies and their use in estimating the average degree of dominance. Biometrics 4:254–266

    Article  CAS  PubMed  Google Scholar 

  18. Cavalli, L. L. (1952). An analysis of linkage in quantitative inheritance

    Google Scholar 

  19. Jinks JL, Hayman BI (1953) The analysis of diallel cross. Maize Genetics News Letter 27:48–54

    Google Scholar 

  20. Gauch HG, Zobel RW (1988) Predictive and postdictive success of statistical analyses of yield trials. Theor Appl Genet 76(1):1–10

    Article  PubMed  Google Scholar 

  21. Kempthorne O (1957) An introduction to genetic statistics. Wiley/Chapman and Hall, New York/London

    Google Scholar 

  22. Hanson WD, Johnson HW (1957) Methods for calculating and evaluating a general selection index obtained by pooling information from two or more experiments. Genetics 42(4):421–432

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Anderson E (1957) A semigraphical method for the analysis of complexproblems. Proc Natl Acad Sci U S A 43(10):923–927

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Dewey DR, Lu K (1959) A correlation and path-coefficient analysis of components of crested wheatgrass seed production 1. Agron J 51(9):515–518

    Article  Google Scholar 

  25. Hayman BI (1958) The separation of epistatic from additive and dominance variation in generation means. Heredity 12:371–390

    Article  Google Scholar 

  26. Jinks JL, Jones RM (1958) Estimation of the components of heterosis. Genetics 43(2):223–234

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Falconer DS (1961) Introduction to quantitative genetics. Pearson Education India

    Google Scholar 

  28. Kearsey MJ, Jinks JL (1968) A general method of detecting additive, dominance and epistatic variation for metrical traits I. Theory Heredity 23(3):403–409

    Article  CAS  Google Scholar 

  29. Rawlings JO, Cockerham CC (1962) Triallel analysis 1. Crop Sci 2(3):228–231

    Article  Google Scholar 

  30. Finlay KW, Wilkinson GN (1963) The analysis of adaptation in a plant-breeding programme. Aust J Agric Res 14(6):742–754

    Article  Google Scholar 

  31. Eberhart ST, Russell WA (1966) Stability parameters for comparing varieties 1. Crop Sci 6(1):36–40

    Article  Google Scholar 

  32. Freeman GH, Perkins JM (1971) Environmental and genotype-environmental components of variability VIII. Relations between genotypes grown in different environments and measures of these environments. Heredity 27(1):15–23

    Article  Google Scholar 

  33. Elston RC, Stewart J (1973) The analysis of quantitative traits for simple genetic models from parental, F1 and backcross data. Genetics 73(4):695–711

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Dudley JW, Moll RH (1969) Interpretation and use of estimates of heritability and genetic variances in plant breeding 1. Crop Sci 9(3):257–262

    Article  Google Scholar 

  35. Cockerham CC (1963) Estimation of genetic variances. Statistical genetics and plant breeding. NAS-NRC 982:53–94

    Google Scholar 

  36. Pearson K (1902) On the fundamental conceptions of biology. Biometrika 1(3):320–344

    Article  Google Scholar 

  37. Smith HF (1936) A discriminant function for plant selection. Ann Eugenics 7(3):240–250

    Article  Google Scholar 

  38. Comstock RE,Moll RH (1963) Genotype environment interactions. Statistical genetics and plant breeding (No. REP-1173. CIMMYT.)

    Google Scholar 

  39. Allard RW, Bradshaw AD (1964) Implications of genotype X environmental interactions in applied plant breeding 1. Crop Sci 4(5):503–508

    Article  Google Scholar 

  40. Lewis D (1954) Gene-environment interaction: a relationship between dominance, heterosis, phenotypic stability and variability. Heredity 8(3):333–356

    Article  Google Scholar 

  41. Wricke G (1964) Zurberechnung der okovalenzbeisommerweizen und hafer. Z Pflanzenzuchtung 52(2):127

    Google Scholar 

  42. Shukla GK (1972) Some statistical aspects of partitioning genotype environmental components of variability. Heredity 29(2):237–245

    Article  CAS  PubMed  Google Scholar 

  43. Gauch HG (1992) Statistical analysis of regional yield trials: AMMI analysis of factorial designs. Elsevier Science Publishers

    Google Scholar 

  44. Freeman GH (1990) Modern statistical methods for analyzing genotype–environment interactions. In: Kang MS (ed) Genotype × environment interaction and plant breeding. Louisiana State University Agricultural Center, Baton Rouge, LA, pp 118–125

    Google Scholar 

  45. Yan W (2001) GGEbiplot—a Windows application for graphical analysis of multienvironment trial data and other types of two way data. Agron J 93(5):1111–1118

    Article  Google Scholar 

  46. Yan W, Kang MS (2002) GGE biplot analysis: a graphical tool for breeders, geneticists, and agronomists. CRC Press

    Book  Google Scholar 

  47. Yan W, Tinker NA (2006) Biplot analysis of multi-environment trial data: principles and applications. Can J Plant Sci 86(3):623–645

    Article  Google Scholar 

  48. Williams EJ (1952) The interpretation of interactions in factorial experiments. Biometrika 39:65–81

    Article  Google Scholar 

  49. Pike EW, Silverberg TR (1952) Designing mechanical computers. Mach Des 24:131–137

    Google Scholar 

  50. Crossa J (1990) Statistical analyses of multilocation trials. In: Advances in agronomy, vol 44. Academic, pp 55–85

    Google Scholar 

  51. Annicchiarico P (1997) Additive main effects and multiplicative interaction (AMMI) analysis of genotype-location interaction in variety trials repeated over years. Theor Appl Genet 94(8):1072–1077

    Article  Google Scholar 

  52. Gauch HG (2006) Statistical analysis of yield trials by AMMI and GGE. Crop Sci 46(4):1488–1500

    Article  Google Scholar 

  53. Neisse AC, Kirch JL, Hongyu K (2018) AMMI and GGE Biplot for genotype× environment interaction: a medoid–based hierarchical cluster analysis approach for high–dimensional data. Biom Lett 55(2):97–121

    Google Scholar 

  54. Lush JL (1943) Animal breeding plans. Animal breeding plans (2nd edn)

    Google Scholar 

  55. Lande R (1976) Natural selection and random genetic drift in phenotypic evolution. Evolution 30:314–334

    Article  PubMed  Google Scholar 

  56. Falconer DS, Mackay TFC (1996) Introduction to quantitative genetics. Pearson Education India

    Google Scholar 

  57. Lynch M, Walsh B (1998) Genetics and analysis of quantitative traits

    Google Scholar 

  58. Heywood JS (2005) An exact form of the breeder’s equation for the evolution of a quantitative trait under natural selection. Evolution 59(11):2287–2298

    PubMed  Google Scholar 

  59. Eberhart SA (1970) Factors affecting efficiencies of breeding methods. Afr Soils 15:669–680

    Google Scholar 

  60. Covarrubias-Pazaran G, Martini JW, Quinn M, Atlin G (2021) Strengthening public breeding pipelines by emphasizing quantitative genetics principles and open source data management. Front Plant Sci 12

    Google Scholar 

  61. Varshney RK, Terauchi R, McCouch SR (2014) Harvesting the promising fruits of genomics: applying genome sequencing technologies to crop breeding. PLoS Biol 12(6):e1001883

    Article  PubMed  PubMed Central  Google Scholar 

  62. Jighly A, Lin Z, Pembleton LW, Cogan NO, Spangenberg GC, Hayes BJ, Daetwyler HD (2019) Boosting genetic gain in allogamous crops via speed breeding and genomic selection. Front Plant Sci 10:1364

    Article  PubMed  PubMed Central  Google Scholar 

  63. Tanksley SD (1993) Mapping polygenes. Annu Rev Genet 27(1):205–233

    Article  CAS  PubMed  Google Scholar 

  64. Lander ES, Botstein D (1989) Mapping mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics 121(1):185–199

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  65. Lincoln SE, Daly MJ, Lander ES (1993) Constructing genetic linkage maps with MAPMAKER/EXP version 3.0: a tutorial and reference manual. A whitehead institute for biomedical research technical report, 3

    Google Scholar 

  66. Utz HF, Melchinger AE (1996) PLABQTL: a program for composite interval mapping of QTL. J Quant Trait Loci 2(1):1–5

    Google Scholar 

  67. Yandell BS, Mehta T, Banerjee S, Shriner D, Venkataraman R, Moon JY et al (2007) R/qtlbim: QTL with Bayesian interval mapping in experimental crosses. Bioinformatics 23(5):641–643

    Article  CAS  PubMed  Google Scholar 

  68. Meng L, Li H, Zhang L, Wang J (2015) QTL IciMapping: integrated software for genetic linkage map construction and quantitative trait locus mapping in biparental populations. Crop J 3:269–283. Go to original source

    Article  Google Scholar 

  69. Ranjan R, Yadav R, Jain N, Sinha N, Bainsla NK, Gaikwad KB, Kumar M (2021) Epistatic QTLsPlay a major role in nitrogen use efficiency and its component traits in Indian spring wheat. Agriculture 11(11):1149

    Article  CAS  Google Scholar 

  70. Chen W, Wang W, Peng M, Gong L, Gao Y, Wan J et al (2016) Comparative and parallel genome-wide association studies for metabolic and agronomic traits in cereals. Nat Commun 2016(7):12767. https://doi.org/10.1038/ncomms12767

    Article  CAS  Google Scholar 

  71. Klein RJ, Zeiss C, Chew EY, Tsai J-Y, Sackler RS, Haynes C, Henning AK et al (2005) Complement factor H polymorphism in age-related macular degeneration. Science 308(5720):385–389

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  72. Bradbury PJ, Zhang Z, Kroon DE, Casstevens TM, Ramdoss Y, Buckler ES (2007) TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics 23(19):2633–2635

    Article  CAS  PubMed  Google Scholar 

  73. Alqudah AM, Sallam A, Baenziger PS, Börner A (2020) GWAS: fast-forwarding gene identification and characterization in temperate cereals: lessons from barley—a review. J Adv Res 22:119–135

    Article  PubMed  Google Scholar 

  74. Zhou X, Stephens M (2012) Genome-wide efficient mixed-model analysis for association studies. Nat Genet 44(7):821–824

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  75. Listgarten J, Lippert C, Heckerman D (2013) FaST-LMM-select for addressing confounding from spatial structure and rare variants. Nat Genet 45(5):470–471

    Article  CAS  PubMed  Google Scholar 

  76. Lippert C, Listgarten J, Liu Y, Kadie CM, Davidson RI, Heckerman D (2011) FaST linear mixed models for genome-wide association studies. Nat Methods 8(10):833–835

    Article  CAS  PubMed  Google Scholar 

  77. Eu-Ahsunthornwattana J, Howey RA, Cordell HJ (2014) Accounting for relatedness in family-based association studies: application to genetic analysis workshop 18 data. In: BMC proceedings, vol 8(1). BioMed Central, p 1–5

    Google Scholar 

  78. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, Bender D et al (2007) PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 81(3):559–575

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  79. Lipka AE, Tian F, Wang Q, Peiffer J, Li M, Bradbury PJ et al (2012) GAPIT: genome association and prediction integrated tool. Bioinformatics 28(18):2397–2399

    Article  CAS  PubMed  Google Scholar 

  80. Wang J, Zhang Z (2018) GAPIT version 3: an interactive analytical tool for genomic association and prediction. Preprint

    Google Scholar 

  81. Hardy OJ, Vekemans X (2002) SPAGeDi: a versatile computer program to analyse spatial genetic structure at the individual or population levels. Mol Ecol Notes 2(4):618–620

    Article  Google Scholar 

  82. Meuwissen TH, Hayes BJ, Goddard ME (2001) Prediction of total genetic value using genome-wide dense marker maps. Genetics 157(4):1819–1829

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  83. Heffner EL, Lorenz AJ, Jannink JL, Sorrells ME (2010) Plant breeding with genomic selection: gain per unit time and cost. Crop Sci 50(5):1681–1690

    Article  Google Scholar 

  84. Wong CK, Bernardo R (2008) Genomewide selection in oil palm: increasing selection gain per unit time and cost with small populations. Theor Appl Genet 116(6):815–824

    Article  CAS  PubMed  Google Scholar 

  85. Singh BD, Singh AK (2015) Marker-assisted plant breeding: principles and practices. Springer, New Delhi, pp 77–122

    Book  Google Scholar 

  86. Heffner EL, Sorrells ME, Jannink JL (2009) Genomic selection for crop improvement. Crop Sci 49:1–12

    Article  CAS  Google Scholar 

  87. Habier D, Fernando RL, Dekkers JC (2007) The impact of genetic relationship information on genome-assisted breeding values. Genetics 177(4):2389–2397

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  88. VanRaden PM (2008) Efficient methods to compute genomic predictions. J Dairy Sci 91(11):4414–4423

    Article  CAS  PubMed  Google Scholar 

  89. Misztal I, Legarra A, Aguilar I (2009) Computing procedures for genetic evaluation including phenotypic, full pedigree, and genomic information. J Dairy Sci 92(9):4648–4655

    Article  CAS  PubMed  Google Scholar 

  90. Speed D, Balding DJ (2014) MultiBLUP: improved SNP-based prediction for complex traits. Genome Res 24(9):1550–1557

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Ranjan, R. et al. (2024). Statistical and Quantitative Genetics Studies. In: Anjoy, P., Kumar, K., Chandra, G., Gaikwad, K. (eds) Genomics Data Analysis for Crop Improvement. Springer Protocols Handbooks. Springer, Singapore. https://doi.org/10.1007/978-981-99-6913-5_4

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  • DOI: https://doi.org/10.1007/978-981-99-6913-5_4

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