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| 1 | Ordering of high-density markers by the k-Optimal algorithm for the traveling-salesman problem显示文摘Construction of accurate and high-density linkage maps is a key research area of genetics.We investigated the efficiency of genetic map construction(MAP)using modifications of the k-Optimal(k-Opt)algorithm for solving the traveling-salesman problem(TSP).For TSP,different initial routes resulted in different optimal solutions.The most optimal solution could be found only by use of as many initial routes as possible.But for MAP,a large number of initial routes resulted in one optimal order.k-Opt using open route length gave a slightly higher proportion of correct orders than the method of adding one virtual marker and using closed route length.Recombination frequency(REC)and logarithm of odds(LOD)score gave similar proportions of correct order,higher than that given by genetic distance.Both missing markers and genotyping error reduced ordering accuracy,but the best order was still achieved with high probability by comparison of the optimal orders from multiple initial routes.Computation time increased rapidly with marker number,and 2-Opt took much less time than 3-Opt.The 2-Opt algorithm was compared with ordering methods used in two other software packages.The best method was 2-Opt using open route length as the criterion to identify the optimal order and using REC or LOD as the measure of distance between markers.We describe a unified software interface for using k-Opt in high-density linkage map construction for a wide range of genetic populations. | Luyan Zhang Huihui Li Lei Meng Jiankang Wang | 2020 | The Crop Journal2020，8，5： | 6 |
| 2 | Linkage analysis and integrated software GAPL for pure-line populations derived from four-way and eight-way crosses显示文摘Pure lines derived from multiple parents provide abundant variation for genetic study.However,efficient genetic analysis methods and user-friendly software are still lacking.In this study, we developed linkage analysis methods and integrated analysis software for pure-line populations derived from four-way and eight-way crosses.First, polymorphic markers are classified into different categories according to the number of identifiable alleles in the inbred parents.Expected genotypic probability is then derived for each pair of complete markers, and based on them a maximum likelihood estimate(MLE) of recombination frequency is calculated.An EM algorithm is proposed for calculating recombination frequencies in scenarios that at least one marker is incomplete.A linkage map can thus be constructed using estimated recombination frequencies.We describe a software package called GAPL for recombination frequency estimation and linkage map construction in multi-parental pure-line populations.Both simulation studies and results from a reported four-way cross recombinant inbred line population demonstrate that the proposed method and software can build more accurate linkage maps in shorter times than other published software packages.The GAPL software is freely available from www.isbreeding.net and can also be used for QTL mapping in multi-parental populations. | Luyan Zhang Lei Meng Jiankang Wang | 2019 | The Crop Journal2019，7，3： | 5 |
| 3 | Identifying genomic regions controlling ratoon stunting disease resistance in sugarcane(Saccharum spp.) clonal F_(1) population显示文摘The ratoon stunting disease (RSD) of sugarcane,caused by the bacterium Leifsonia xyli subsp.xyli,is one of the major concerns to sugarcane production and breeding programs worldwide.Due to no obvious external symptoms,RSD cannot be easily detected by the growers,hence has reduced the world’s sugarcane production significantly.This study aimed to identify quantitative trait loci (QTL) associated with RSD resistance and to assist in the development of linked molecular markers for marker-assisted breeding to minimize the reduction in sugarcane yield by the RSD infection.A set of 146 individuals derived from a self-crossing of CP80-1827 were evaluated for RSD resistance in a mechanically duplicated inoculated field trial from 2014 to 2017 using tissue blot immunoassay.Leveraging the genetic data and the four years phenotyping data of CP80-1827 selfing population,linkage map construction and QTL analysis were conducted based on clonal F_1 and F_2 mapping population types with GACD V.1.2 and Ici Mapping V.3.3,respectively.A total of 23 QTL associated with RSD resistance were identified,which explained 6%to13%of the phenotypic variation with the two types of software.A total of 82 disease resistance genes were identified by searching these 23 QTL regions on their corresponding regions on the Sorghum bicolor genome (44 genes),sugarcane R570 genome (20 genes),and S.spontaneum genome (18 genes),respectively.Compared with Ici Mapping V.3.3,GACD V.1.2 identified more major (6 vs.3) and stable QTL (2vs.0),and more disease resistance genes (51 vs.31),indicating GACD V.1.2 (clonal F_1 mapping type) is most likely to be more efficient than Ici Mapping (F_2 mapping type) for QTL analysis of a sefling population or clonal F_1 population in clonal species.The identified QTL controlling RSD resistance along with the associated SNP markers will assist sugarcane molecular breeding programs in combating this disease. | Qian You Sushma Sood Ziliang Luo Hongbo Liu Md.Sariful Islam Muqing Zhang Jianping Wang | 2021 | The Crop Journal2021，9，5： | 1 |
| 4 | Quantitative genetic studies with applications in plant breeding in the omics era显示文摘Quantitative genetics is concerned with the inheritance of biological traits showing continuous(or quantitative)phenotypic variation.Quantitative traits are common and have been extensively investigated and studied in evolutionary and genetic studies and in plant and animal breeding.Quantitative traits are normally controlled by multiple genes with various kinds of genetic effect,and their phenotypes are readily modified by environmental variation. | Jiankang Wang JoséCrossa Junyi Gai | 2020 | The Crop Journal2020，8，5： | 0 |
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