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.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
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
Galton F (1889) Natural Inheritance Macmillan & Co
Pearson K (1894) Contributions to the mathematical theory of evolution. Philos Trans R Soc London A 185:71–110
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
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
Johannsen W (1903) Ueber Erblichkeit in Populationen und in reinen Linien: ein Beitrag zur Beleuchtung schwebender Selektionsfragen. G. Fischer
Nilsson-Ehle H (1909) Kreuzungsuntersuchungen an hafer und weizen, vol 5(2). H. Ohlssonsbuchdruckerei
East EM (1916) Studies on size inheritance in Nicotiana. Genetics 1(2):164–176
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
Wright S (1921) Systems of mating. I. The biometric relations between parent and offspring. Genetics 6(2):111–123
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
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
Mahalanobis PC (1928) Statistical study of the Chinese head. Proceedings of the Indian science congress (Calcutta)
Sprague GF, Tatum LA (1942) General vs. specific combining ability in single crosses of corn. J Am Soc Agron 34:923–932
Malécot G (1948) Les Mathématiques de l’Hérédité. Masson, Paris. (translated as The Mathematics of Heredity)
Mather K (1949) Biometrical genetics. Methuen and Co. Ltd., London, p 162
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
Cavalli, L. L. (1952). An analysis of linkage in quantitative inheritance
Jinks JL, Hayman BI (1953) The analysis of diallel cross. Maize Genetics News Letter 27:48–54
Gauch HG, Zobel RW (1988) Predictive and postdictive success of statistical analyses of yield trials. Theor Appl Genet 76(1):1–10
Kempthorne O (1957) An introduction to genetic statistics. Wiley/Chapman and Hall, New York/London
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
Anderson E (1957) A semigraphical method for the analysis of complexproblems. Proc Natl Acad Sci U S A 43(10):923–927
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
Hayman BI (1958) The separation of epistatic from additive and dominance variation in generation means. Heredity 12:371–390
Jinks JL, Jones RM (1958) Estimation of the components of heterosis. Genetics 43(2):223–234
Falconer DS (1961) Introduction to quantitative genetics. Pearson Education India
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
Rawlings JO, Cockerham CC (1962) Triallel analysis 1. Crop Sci 2(3):228–231
Finlay KW, Wilkinson GN (1963) The analysis of adaptation in a plant-breeding programme. Aust J Agric Res 14(6):742–754
Eberhart ST, Russell WA (1966) Stability parameters for comparing varieties 1. Crop Sci 6(1):36–40
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
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
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
Cockerham CC (1963) Estimation of genetic variances. Statistical genetics and plant breeding. NAS-NRC 982:53–94
Pearson K (1902) On the fundamental conceptions of biology. Biometrika 1(3):320–344
Smith HF (1936) A discriminant function for plant selection. Ann Eugenics 7(3):240–250
Comstock RE,Moll RH (1963) Genotype environment interactions. Statistical genetics and plant breeding (No. REP-1173. CIMMYT.)
Allard RW, Bradshaw AD (1964) Implications of genotype X environmental interactions in applied plant breeding 1. Crop Sci 4(5):503–508
Lewis D (1954) Gene-environment interaction: a relationship between dominance, heterosis, phenotypic stability and variability. Heredity 8(3):333–356
Wricke G (1964) Zurberechnung der okovalenzbeisommerweizen und hafer. Z Pflanzenzuchtung 52(2):127
Shukla GK (1972) Some statistical aspects of partitioning genotype environmental components of variability. Heredity 29(2):237–245
Gauch HG (1992) Statistical analysis of regional yield trials: AMMI analysis of factorial designs. Elsevier Science Publishers
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
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
Yan W, Kang MS (2002) GGE biplot analysis: a graphical tool for breeders, geneticists, and agronomists. CRC Press
Yan W, Tinker NA (2006) Biplot analysis of multi-environment trial data: principles and applications. Can J Plant Sci 86(3):623–645
Williams EJ (1952) The interpretation of interactions in factorial experiments. Biometrika 39:65–81
Pike EW, Silverberg TR (1952) Designing mechanical computers. Mach Des 24:131–137
Crossa J (1990) Statistical analyses of multilocation trials. In: Advances in agronomy, vol 44. Academic, pp 55–85
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
Gauch HG (2006) Statistical analysis of yield trials by AMMI and GGE. Crop Sci 46(4):1488–1500
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
Lush JL (1943) Animal breeding plans. Animal breeding plans (2nd edn)
Lande R (1976) Natural selection and random genetic drift in phenotypic evolution. Evolution 30:314–334
Falconer DS, Mackay TFC (1996) Introduction to quantitative genetics. Pearson Education India
Lynch M, Walsh B (1998) Genetics and analysis of quantitative traits
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
Eberhart SA (1970) Factors affecting efficiencies of breeding methods. Afr Soils 15:669–680
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
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
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
Tanksley SD (1993) Mapping polygenes. Annu Rev Genet 27(1):205–233
Lander ES, Botstein D (1989) Mapping mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics 121(1):185–199
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
Utz HF, Melchinger AE (1996) PLABQTL: a program for composite interval mapping of QTL. J Quant Trait Loci 2(1):1–5
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
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
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
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
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
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
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
Zhou X, Stephens M (2012) Genome-wide efficient mixed-model analysis for association studies. Nat Genet 44(7):821–824
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
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
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
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
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
Wang J, Zhang Z (2018) GAPIT version 3: an interactive analytical tool for genomic association and prediction. Preprint
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
Meuwissen TH, Hayes BJ, Goddard ME (2001) Prediction of total genetic value using genome-wide dense marker maps. Genetics 157(4):1819–1829
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
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
Singh BD, Singh AK (2015) Marker-assisted plant breeding: principles and practices. Springer, New Delhi, pp 77–122
Heffner EL, Sorrells ME, Jannink JL (2009) Genomic selection for crop improvement. Crop Sci 49:1–12
Habier D, Fernando RL, Dekkers JC (2007) The impact of genetic relationship information on genome-assisted breeding values. Genetics 177(4):2389–2397
VanRaden PM (2008) Efficient methods to compute genomic predictions. J Dairy Sci 91(11):4414–4423
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
Speed D, Balding DJ (2014) MultiBLUP: improved SNP-based prediction for complex traits. Genome Res 24(9):1550–1557
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2024 The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd.
About this protocol
Cite this protocol
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
Download citation
DOI: https://doi.org/10.1007/978-981-99-6913-5_4
Published:
Publisher Name: Springer, Singapore
Print ISBN: 978-981-99-6912-8
Online ISBN: 978-981-99-6913-5
eBook Packages: Springer Protocols