Development of <Emphasis Type="Italic">Gossypium barbadense</Emphasis> chromosome segment substitution lines in the genetic standard line TM-1 of <Emphasis Type="Italic">Gossypium hirsutum</Emphasis>

Chromosome segment substitution lines （CSSL） consist of a battery of near-isogenic lines that have been developed and cover the entire genome of some crops. With the exception of one homozygous chromosome segment transferred from a donor parent, the remaining genome of each CSSL line is the same as the recipient parent. It is an ideal material for genome research and particularly QTL mapping. In the present study, we first developed one set of CSSL lines using G hirsutum acc. TM-1 （the genetic standard）, as the recipient parent and G barbadense cv. Hai7124 as the donor parent using molecular assistedlselection in BC5S1-3 generations. The CSSL consisted of 330 different lines, in which 1-4 different lines had the same or overlapping substituted segments. The genetic length of the substituted segments covered 5271.9 cM with an average segment distance of 10.9 cM, 1.5 times the total genetic length of Upland cotton （3514.6 cM）. The substituted segments of each line varied in length, ranging from 3.5 cM for the shortest segment to 23.2 cM in the longest segment. Our CSSL have not yet to cover the entire tetraploid cotton genome, due to the absence of some donor parent interval segments.     

Study on heterosis of intersubspecies between indica and japonica rice （Oryza sativa L.） using chromosome segment substitution lines

Great heterosis exists in the inter-subspecific crossesbetween indica and japonica rice cultivars[1,2] and the ex-ploitation of this heterosis has long been considered as apromising method to further increase rice yield potential[3].Previous studies indicated that there were large differencesbetween the two subspecies with respect to morphology,isozyme, polymorphism of molecular markers and DNAstructure due to long time genetic differentiation[4,5]. Thosedifferences were identified to be clos…     

Bin-based model construction and analytical strategies for dissecting complex traits with chromosome segment substitution lines

Chromosome segment substitution lines have been created in several experimental models,including many plant and animal species,and are useful tools for the genetic analysis and mapping of complex traits.The traditional t-test is usually applied to identify a quantitative trait locus (QTL) that is contained within a chromosome segment to estimate the QTL’s effect.However,current methods cannot uncover the entire genetic structure of complex traits.For example,current methods cannot distinguish between main effects and epistatic effects.In this paper,a linear epistatic model was constructed to dissect complex traits.First,all the long substituted segments were divided into overlapping small bins,and each small bin was considered a unique independent variable.The genetic model for complex traits was then constructed.When considering all the possible main effects and epistatic effects,the dimensions of the linear model can become extremely high.Therefore,variable selection via stepwise regression (Bin-REG) was proposed for the epistatic QTL analysis in the present study.Furthermore,we tested the feasibility of using the LASSO (least absolute shrinkage and selection operator) algorithm to estimate epistatic effects,examined the fully Bayesian SSVS (stochastic search variable selection) approach,tested the empirical Bayes (E-BAYES) method,and evaluated the penalized likelihood (PENAL) method for mapping epistatic QTLs.Simulation studies suggested that all of the above methods,excluding the LASSO and PENAL approaches,performed satisfactorily.The Bin-REG method appears to outperform all other methods in terms of estimating positions and effects.