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| 1 | Sequencing a Juglans regia×J.microcarpa hybrid yields high-quality genome assemblies of parental species显示文摘Members of the genus Juglans are monecious wind-pollinated trees in the family Juglandaceae with highly heterozygous genomes,which greatly complicates genome sequence assembly.The genomes of interspecific hybrids are usually comprised of haploid genomes of parental species.We exploited this attribute of interspecific hybrids to avoid heterozygosity and sequenced an interspecific hybrid Juglans microcarpa×J.regia using a novel combination of single-molecule sequencing and optical genome mapping technologies.The resulting assemblies of both genomes were remarkably complete including chromosome termini and centromere regions.Chromosome termini consisted of arrays of telomeric repeats about 8 kb long and heterochromatic subtelomeric regions about 10 kb long.The centromeres consisted of arrays of a centromere-specific Gypsy retrotransposon and most contained genes,many of them transcribed.Juglans genomes evolved by a whole-genome-duplication dating back to the Cretaceous-Paleogene boundary and consist of two subgenomes,which were fractionated by numerous short gene deletions evenly distributed along the length of the chromosomes.Fractionation was shown to be asymmetric with one subgenome exhibiting greater gene loss than the other.The asymmetry of the process is ongoing and mirrors an asymmetry in gene expression between the subgenomes.Given the importance of J.microcarpa×J.regia hybrids as potential walnut rootstocks,we catalogued disease resistance genes in the parental genomes and studied their chromosomal distribution.We also estimated the molecular clock rates for woody perennials and deployed them in estimating divergence times of Juglans genomes and those of other woody perennials. | Tingting Zhu Le Wang Frank M.You Juan C.Rodriguez Karin R.Deal Limin Chen Jie Li Sandeep Chakraborty Bipin Balan Cai-Zhong Jiang Patrick J.Brown Charles ALeslie Mallikarjuna KAradhya Abhaya M.Dandekar Patrick E.McGuire Daniel Kluepfel Jan Dvorak Ming-Cheng Luo | 2019 | Horticulture Research2019，6，1： | 7 |
| 2 | Estimation of genetic parameters and their sampling variances for quantitative traits in the type 2 modified augmented design显示文摘The type 2 modified augmented design(MAD2) is an efficient unreplicated experimental design used for evaluating large numbers of lines in plant breeding and for assessing genetic variation in a population. Statistical methods and data adjustment for soil heterogeneity have been previously described for this design. In the absence of replicated test genotypes in MAD2, their total variance cannot be partitioned into genetic and error components as required to estimate heritability and genetic correlation of quantitative traits, the two conventional genetic parameters used for breeding selection. We propose a method of estimating the error variance of unreplicated genotypes that uses replicated controls, and then of estimating the genetic parameters. Using the Delta method, we also derived formulas for estimating the sampling variances of the genetic parameters.Computer simulations indicated that the proposed method for estimating genetic parameters and their sampling variances was feasible and the reliability of the estimates was positively associated with the level of heritability of the trait. A case study of estimating the genetic parameters of three quantitative traits, iodine value, oil content, and linolenic acid content, in a biparental recombinant inbred line population of flax with 243 individuals, was conducted using our statistical models. A joint analysis of data over multiple years and sites was suggested for genetic parameter estimation. A pipeline module using SAS and Perl was developed to facilitate data analysis and appended to the previously developed MAD data analysis pipeline(http://gffzzebd7c0d4fd3c45a1hkpnqxbwno5uv6xub.ffgz.tsg.suse.edu.cn/bioinformatics_ tools/MADPipeline/index.html). | Frank M.You Qijian Song Gaofeng Jia Yanzhao Cheng Scott Duguid Helen Booker Sylvie Cloutier | 2016 | The Crop Journal2016，4，2： | 1 |
| 3 | Accuracy of genomic selection in biparental populations of flax(Linum usitatissimum L.)显示文摘Flax is an important economic crop for seed oil and stem fiber. Phenotyping of traits such as seed yield, seed quality, stem fiber yield, and quality characteristics is expensive and time consuming. Genomic selection(GS) refers to a breeding approach aimed at selecting preferred individuals based on genomic estimated breeding values predicted by a statistical model based on the relationship between phenotypes and genome-wide genetic markers. We evaluated the prediction accuracy of GS(rMP) and the efficiency of GS relative to phenotypic selection(RE) for three GS models: ridge regression best linear unbiased prediction(RR-BLUP),Bayesian LASSO(BL), and Bayesian ridge regression(BRR), for seed yield, oil content, iodine value, linoleic, and linolenic acid content with a full and a common set of genome-wide simple sequence repeat markers in each of three biparental populations. The three GS models generated similar rMPand RE, while BRR displayed a higher coefficient of determination(R^2)of the fitted models than did RR-BLUP or BL. The mean rMPand RE varied for traits with different heritabilities and was affected by the genetic variation of the traits in the populations.GS for seed yield generated a mean RE of 1.52 across populations and marker sets, a value significantly superior to that for direct phenotypic selection. Our empirical results provide the first validation of GS in flax and demonstrate that GS could increase genetic gain per unit time for linseed breeding. Further studies for selection of training populations and markers are warranted. | Frank M.You Helen M.Booker Scott D.Duguid Gaofeng Jia Sylvie Cloutier | 2016 | The Crop Journal2016，4，4： | 0 |
| 4 | Inheritance of marsh spot disease resistance in cranberry common bean(Phaseolus vulgaris L.)显示文摘Common bean(Phaseolus vulgaris) is an annual legume crop that is grown worldwide for its edible dry seeds and tender pods. Marsh spot(MS) of the seeds is a physio-genic stress disease affecting seed quality in beans. Studies have suggested that this disease involves a nutritional disorder caused by manganese deficiency, but the inheritance of resistance to this disease has not been reported. A biparental genetic population composed of 138 recombinant inbred lines(RILs) was developed from a cross between an MS resistant cultivar ‘Cran09’ and an MS susceptible cultivar ‘Messina’. The 138 RILs and their two parents were evaluated for MS resistance during five consecutive years from 2015 to 2019 in sandy and heavy clay soils in Morden, Manitoba, Canada. The MS incidence(MSI) and the MS resistance index(MSRI) representing disease severity were shown to be both highly correlated heritable traits that had high broad-sense heritability values(H;) of 86.5% and 83.2%, respectively. No significant differences for MSI and MSRI were observed between the two soil types in all five-(MSI) or four-year(MSRI) data collection, but significant correlations among years were observed despite MS resistance was moderately affected by year. The MSIs and MSRIs displayed a right-skewed distribution, indicating a mixed genetic model involving a few major genes and polygenes. Using the joint segregation analysis method, the same four major genes with additive-epistasis effects showed the best fit for both traits, explaining 84.4% and85.3% of the phenotypic variance for MSI and MSRI, respectively. For both traits, the M1, M2, M3 and m4 acted as the favorable(resistant) alleles for the four genes where M and m represent two alleles of each gene. However, due to epistatic effects, only the individuals of the M1 M2 M3 M4 haplotype appeared to be highly resistant, whereas those of the m1 m2 m3 M4 haplotype were the most susceptible. The m4 allele significantly suppressed the additive effects of M1 M2 M3 on resistance, but decreased susceptibility due to the additive effects of m1 m2 m3. Further quantitative trait locus(QTL) mapping is warranted to identify and validate individual genes and develop molecular markers for marker-assisted selection of resistant cultivars. | Bosen Jia Robert L.Conner Nadeem Khan Anfu Hou Xuhua Xia Frank M.You | 2022 | The Crop Journal2022，10，2： | 0 |
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