Pedigree in humans and wheat
Pedigree information include information about ancestry. Keeping pedigree records is a centuries-old tradition. Pedigrees can also be verified using gene-marker data.In plants
The method has been discussed in the context of plant breeding populations. Pedigree records are kept by plants breeders and pedigree-based selection is popular in several plant species. Plant pedigrees are different from that of humans, particularly as plant are hermaphroditic – an individual can be male or female and mating can be performed in random combinations, with inbreeding loops. Also plant pedigrees may contain of "selfs", i.e. offspring resulting from self-pollination of a plant.Pedigree denotation
SIMPLE CROSS SYMBOL Example / first order cross SON 64/KLRE //, second order cross IR 64/KLRE // CIAN0 /3/, third order cross TOBS /3/ SON 64/KLRE // CIAN0 /4/, fourth order cross TOBS /3/ SON 64/KLRE // CIAN0 /4/ SEE /n/, nth order cross BACK CROSS SYMBOL *n n number of times the back cross parent used left side simple cross symbol, back cross parent is the female, right side – male, Example: SEE/3*ANE, TOBS*6/CIAN0 The idea of family-based QTL mapping comes from inheritance of marker alleles and its association with trait of interest has demonstrated how to use family-based association in plant breeding families.Limitation of conventional methods
Traditional mapping populations include single family consisting of crossing between two parents or three parents often distantly related. There are some important limitations associated with traditional mapping methods. Some of which include limited polymorphism rates, and no indication of marker effectiveness in multiple genetic backgrounds. Often, by the time a QTL mapping population is developed and mapped, breeders have introgressed the new QTL using traditional breeding and selection methods. This can reduce the usefulness of MAS (marker-assisted selection) within breeding programs at the time when MAS could be most useful (i.e., shortly after new QTL are identified). Family-based QTL mapping removes this limitation by using existing plant breeding families.Common study population mapping
Broadly, there are 3 classes of study designs: study designs in which large sets of relatives from extended or nuclear families are sampled, study designs in which pairs of relatives are sampled (e.g., sibling pairs) or study designs in which unrelated individuals are sampled.Unrelated individuals
Natural collection of individuals (considered unrelated) with unknown pedigree constitutes mapping populations. The population based association mapping technique are based on this type of populations. In plant context such population are hard to find as most of individuals are someway related. Other disadvantage of such method is that even if we can find such a population, it is difficult to find high allele frequency for allele of interest (usually mutant)in such situation. For purpose of create balance in allele frequency, usually case-control studies.Sibpairs
Such design include a pair of sibs from multiple independent families. The members in each sibpairs are not randomly chosen – often both siblings are chosen from one tail (upper or lower) of the distribution of the QT (concordant siblings) or one sibling is chosen from the upper tail and the other sibling is chosen from the lower tail (discordant siblings). Another sampling design could include a pair of siblings, one chosen from the upper or lower tail of the distribution and the other chosen randomly from among the remaining siblings.Trios
Trios include parents and one offspring (most affected). Trios are more commonly used in association studies. The concept of association mapping that each trio are unrelated, however trios are related in themselves.Nuclear family
Nuclear family consists of two generation simple family pedigree.Extended pedigrees
In extended pedigree include multiple generation pedigree. It can be as deep or wide as the pedigree information is available. Extended pedigree are attractive for linkage-based analysis.Linkage vs association analysis
Linkage and association analysis are primary tools for gene discovery, localization and functional analysis. While conceptual underpinning of these approaches have been long known, advances in recent decades inFamily-based linkage analysis
Genetic linkage is the phenomenon where by alleles at different loci cosegregate in families. The strength of cosegregation is measured by the recombination fraction θ, the probability of an odd number of recombination. More complex pedigree provide higher power.Family-based association analysis
Linkage disequilibrium (LD) and association mapping is receiving considerable attention in the plant genetics community for its potential to use existing genetic resources collections to fine map quantitative trait loci (QTL), validate candidate genes, and identify alleles of interest (Yu and Buckler, 2006). The three elements of particular importance for conducting association mapping or interpreting the results include: # the analysis of population structure into subgroups, # its use to control for spurious associations and consequences in the specific case of differential selection among subgroups, and # the analysis of the local structure of LD intoQuantitative transmission disequilibrium test (QTDT)
The TDT has been extended in context of quantitative traits and nuclear or extended pedigree families. The generalized test allows to use any family type of families in testing. QTDT has also be been extended to haplotype-based association mapping.Drawing family pedigrees
There are several pedigree drawing software available for human genetics context such as COPE (COllaborative Pedigree drawing Environment), CYRILLIC, FTM (Family Tree Maker), FTREE, KINDRED, PED (PEdigree Drawing software),PEDHUNTER, PEDIGRAPH, PEDIGREE/DRAW, PEDIGREE-VISUALIZER, PEDPLOT,PEDRAW/WPEDRAW (Pedigree Drawing/ Window Pedigree Drawing (MS-Window and X-Window version of PEDRAW)), PROGENY (Progeny Software, LLC) etc. However the pedigree drawing in plants requires some additional features such as inbreeding, selfing, mutation, polyploidy etc. which is supported iSee also
*References
{{reflist, refs= {{Cite journal , last1 = Rosyara , first1 = U. R. , last2 = Gonzalez-Hernandez , first2 = J. L. , last3 = Glover , first3 = K. D. , last4 = Gedye , first4 = K. R. , last5 = Stein , first5 = J. M. , title = Family-based mapping of quantitative trait loci in plant breeding populations with resistance to Fusarium head blight in wheat as an illustration , doi = 10.1007/s00122-009-1010-9 , journal = Theoretical and Applied Genetics , volume = 118 , issue = 8 , pages = 1617–1631 , year = 2009 , pmid = 19322557, s2cid = 2882803 Beavis W.D. (1998) "QTL analyses: power, precision, and accuracy". In: Paterson AH (ed) ''Molecular analysis of complex traits''. CRC Press, Boca Raton, pp 145–161 {{Cite journal , last1 = Lander , first1 = E. S. , last2 = Green , first2 = P. , title = Construction of multilocus genetic linkage maps in humans , journal = Proceedings of the National Academy of Sciences of the United States of America , volume = 84 , issue = 8 , pages = 2363–2367 , year = 1987 , pmid = 3470801 , pmc = 304651 , doi=10.1073/pnas.84.8.2363 , bibcode = 1987PNAS...84.2363L , doi-access = free Glazier AM, Nadeau JH, Aitman TJ (2002) "Finding genes that underlie complex traits". ''Science'' 298:2345–2349 * Yu J, Buckler ES (2006) "Genetic association mapping and genome organization of maize". ''Curr Opin Biotechnol'' 17:155–160 * Flint-Garcia S, Thornsberry JM, Buckler ESIV (2003) "Structure of linkage disequilibrium in plants". ''Annu Rev Plant Biol'' 54:357–374 Statistical genetics