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非交叉配子形成体的连锁图谱构建方法(英文)

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Acta Genetica Sinica 2005年第6期32卷 608-615页

作者：吴吉祥朱军 johnie N.jenkins Jack C.McCarty 浙江大学农业与生物技术学院美国密西西比州立大学植物土壤系密西西比39762 美国农部作物研究室

根据非交叉(achiasmatic)遗传模型,提出采用最大似然法计算遗传交换率的方法,同时开发了构建非交叉生物(F2群体)连锁图谱的计算机软件。通过卡方验检可测性连锁分子标记。对于无交叉生物现象,采用蒙特卡洛模拟技术,对交叉(chiasmatic)... 详细信息

根据非交叉(achiasmatic)遗传模型,提出采用最大似然法计算遗传交换率的方法,同时开发了构建非交叉生物(F2群体)连锁图谱的计算机软件。通过卡方验检可测性连锁分子标记。对于无交叉生物现象,采用蒙特卡洛模拟技术,对交叉(chiasmatic)和非交叉两个遗传模型遗传交换率的估计值和作图效率进行了比较。模拟结果表明,非交叉模型能提供无偏的估计值,而交叉模型则只有实际值的一半。在所有同等的条件下,基于非交叉模型的作图效率均高于基于交叉模型(无校正)的作图效率。对于非交叉配子形成体,采用基于非交叉模型的交换率计算方法能获得理想的作图效率。

关键词：连锁作图性连锁非交叉配子发生最大似然法

Evaluation of Moving Grid Adjustment (MGA) Method in Field Variation Control

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Open Journal of Statistics 2024年第5期14卷 450-466页

作者： Jixiang Wu johnie N. jenkins Jack C. McCarty Genetics and Sustainable Agriculture Research Unit USDA-ARS Mississippi State MS USA

Spatial variation is often encountered when large scale field trials are conducted which can result in biased estimation or prediction of treatment (i.e. genotype) values. An effective removal of spatial variation is needed to ensure unbiased estimation or prediction and thus increase the accuracy of field data evaluation. A moving grid adjustment (MGA) method, which was proposed by Technow, was evaluated through Monte Carlo simulation for its statistical properties regarding field spatial variation control. Our simulation results showed that the MGA method can effectively account for field spatial variation if it does exist;however, this method will not change phenotype results if field spatial variation does not exist. The MGA method was applied to a large-scale cotton field trial data set with two representative agronomic traits: lint yield (strong field spatial pattern) and lint percentage (no field spatial pattern). The results suggested that the MGA method was able to effectively separate the spatial variation including blocking effects from random error variation for lint yield while the adjusted data remained almost identical to the original phenotypic data. With application of the MGA method, the estimated variance for residuals was significantly reduced (62.2% decrease) for lint yield while more genetic variation (29.7% increase) was detected compared to the original data analysis subject to the conventional randomized complete block design analysis. On the other hand, the results were almost identical for lint percentage with and without the application of the MGA method. Therefore, the MGA method can be a useful addition to enhance data analysis when field spatial pattern exists.

关键词： Spatial Variation Linear Mixed Model Approach Experimental Design Moving Grid Adjustment Crop Trial

Constructing Molecular Marker Linkage Maps of Chromosome 14Sh and 22Sh and QTL Mapping for Major Traits by Use of Substitution Lines of Gossypium hirsutum L.

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棉花学报 2008年第S1期20卷 85-页

作者： SAHA Sukumar jenkins johnie N USDA-ARS Crop Science Research Laboratory Mississippi State

CSB14Sh,which is isogenic for its recurrent parent TM-1 except for chromosome 14 short arm,was crossed with TM-1,and the F2 population was produced.A total of 3800 SSR primer pairs covering the whole genome were used ... 详细信息

关键词： QTLs Constructing Molecular Marker Linkage Maps of Chromosome 14Sh and 22Sh and QTL Mapping for Major Traits by Use of Substitution Lines of Gossypium hirsutum L

Comparison of REML and MINQUE for Estimated Variance Components and Predicted Random Effects

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Open Journal of Statistics 2016年第5期6卷 814-823页

作者： Nan Nan johnie N. jenkins Jack C. McCarty Jixiang Wu Department of Mathematics and Statistics South Dakota State University Brookings SD USA Crop Science Research Laboratory USDA-ARS Mississippi State MS USA Agronomy Horticulture and Plant Science Department South Dakota State University Brookings SD USA

Linear mixed model (LMM) approaches have been widely applied in many areas of research data analysis because they offer great flexibility for different data structures and linear model systems. In this study, emphasis is placed on comparing the properties of two LMM approaches: restricted maximum likelihood (REML) and minimum norm quadratic unbiased estimation (MINQUE) with and without resampling techniques being included. Bias, testing power, Type I error, and computing time were compared between REML and MINQUE approaches with and without Jackknife technique based on 500 simulated data sets. Results showed that MINQUE and REML methods performed equally regarding bias, Type I error, and power. Jackknife-based MINQUE and REML greatly improved power compared to non-Jackknife based linear mixed model approaches. Results also showed that MINQUE is more time-saving compared to REML, especially with the use of resampling techniques and large data set analysis. Results from the actual cotton data analysis were in agreement with our simulated results. Therefore, Jackknife-based MINQUE approaches could be recommended to achieve desirable power with reduced time for a large data analysis and model simulations.

关键词： Comparison of REML and MINQUE for Estimated Variance Components and Predicted Random Effects

An Adaptive Sequential Replacement Method for Variable Selection in Linear Regression Analysis

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Open Journal of Statistics 2023年第5期13卷 746-760页

作者： Jixiang Wu johnie N. jenkins Jack C. McCarty Jr. Genetics and Sustainable Agriculture Research Unit USDA-ARS Mississippi State USA

With the rapid development of DNA technologies, high throughput genomic data have become a powerful leverage to locate desirable genetic loci associated with traits of importance in various crop species. However, current genetic association mapping analyses are focused on identifying individual QTLs. This study aimed to identify a set of QTLs or genetic markers, which can capture genetic variability for marker-assisted selection. Selecting a set with k loci that can maximize genetic variation out of high throughput genomic data is a challenging issue. In this study, we proposed an adaptive sequential replacement (ASR) method, which is considered a variant of the sequential replacement (SR) method. Through Monte Carlo simulation and comparing with four other selection methods: exhaustive, SR method, forward, and backward methods we found that the ASR method sustains consistent and repeatable results comparable to the exhaustive method with much reduced computational intensity.

关键词： Adaptive Sequential Replacement Association Mapping Exhaustive Method Global Optimal Solution Sequential Replacement Variable Selection

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中美几个棉花品种育种应用价值研究(英文)

棉花学报 2005年第1期17卷 47-55页

作者： McCARTY Jack C WU Ji-xiang jenkins johnie N 郭香墨 USDA ARS Crop Science Research Laboratory Mississippi State MS USA Department of Plant and Soil Sciences Mississippi State University Mississippi State MS USA 中国农业科学院棉花研究所

用3个美国陆地棉品种为母本与2个中国品种配制6个杂交组合。5个亲本与其6个杂交组合F2和F3种植在美国密西西比州立大学农业试验站。利用加性显性加×加互作遗传模型(ADAA)进行数据分析。结果表明,除了加性和显性效应外,加×加互作效... 详细信息

用3个美国陆地棉品种为母本与2个中国品种配制6个杂交组合。5个亲本与其6个杂交组合F2和F3种植在美国密西西比州立大学农业试验站。利用加性显性加×加互作遗传模型(ADAA)进行数据分析。结果表明,除了加性和显性效应外,加×加互作效应控制大多数农艺性状和纤维性状。两个中国品种均可用于纤维麦克隆值的改良。品种CR110及Deltapine90(DP90)在纤维长度和强度方面具有较好的一般配合力。与品种DP90的杂交组合可以在较晚世代用于产量的改良。杂交组合Stoneville474(ST474)×CR110可用于在早期提高皮棉产量。除ST474×CR110之外,其它各组合均具有产量改良的潜力。组合Sure Grow747(SG747)×86 1在早期和晚期均比其它组合有较高的纤维强度。考虑到皮棉和纤维品质的基因型值,组合SG747×86 1可用于提高早期和晚期产量的改良且有好的纤维品质。

关键词：杂交组合中国品种纤维品质棉花品种改良育种加性产量中美 ST

Characterization of a Novel RING-Type Ubiquitin E3 Ligase GhRING2 Differentially Expressed in Cotton Fiber

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American Journal of Plant Sciences 2014年第21期5卷 3364-3379页

作者： Shiva Soma Chuan-Yu Hsu Sukumar Saha johnie N. jenkins Din-Pow Ma Department of Biochemistry Molecular Biology Entomology and Plant Pa-thology Mississippi State University Mississippi State USA Institute for Genomics Biocomputing & Biotechnology Mississippi State Uni-versity Mississippi State USA Crop Science Research Laboratory Agricultural Research Service United States Department of Agriculture Mississippi State USA Department of Plant and Soil Sciences Mississippi State University Mississippi State USA

The ubiquitin-proteasome proteolysis pathway is responsible for the degradation of abnormal and short-lived proteins to regulate many important biochemical activities in eukaryotes. By employing affymetrix microarray analysis, we have identified a novel ubiquitin ligase E3 gene GhRING2 that is differentially expressed between two Gossypium hirsutum lines-Texas Marker-1 (TM-1) and Chromosome Substitution Line CS-B25. The CS-B25 line has chromosome 25 from G. barbadense substituted into TM-1. The complete nucleotide sequences of GhRING2 along with its 5’-flanking region were obtained by genomic walking. GhRING2 was highly expressed in elongating fiber, and GUS expression directed by the GhRING2 promoter was found in hypocotyls and young stems of transgenic Arabidopsis plants. Using a yeast two-hybrid assay GhRING2 was found to interact with a PROTODERMAL FACTOR1 (GhPDF1) protein. GhPDF1 was expressed preferentially in immature ovules and fiber initials, and the GhPDF1 gene had been suggested to play a role in cell fate determination and fiber development. Pull down and plasmid swap assays further confirmed the interaction between GhRING2 and GhPDF1. The expression and protein interaction data indicate that GhRING2 may be involved in the turnover of GhPDF1 and participation in the transition from initiation to elongation stages during fiber development. Our data strongly suggest that the ubiquitin-proteasome pathway may regulate cotton fiber growth and development. The nucleotide sequence data of GhRING2 in this article have been submitted to the Gen Bank Nucleotide Sequence Data Bases under the accession number BankIt 1,742,008 SeqKM 108,000.

关键词： Cotton Fiber Gossypium hirsutum G. barbadense RING-Type Ubiquitin Ligase Ubiquitination

Effects of Plant Density on Boll Retention and Yield of Cotton in the Mid-South

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American Journal of Plant Sciences 2017年第4期8卷 891-906页

作者： Jack C. McCarty johnie N. jenkins Russell W. Hayes Martin J. Wubben Genetics and Sustainable Agriculture Research Unit Crop Science Research Laboratory USDA-ARS Starkville MS USA

The number of cotton (Gossypium hirsutum L.) plants being grown per unit of land area has gained attention due to the technology fees associated with seed containing value added traits. We investigated boll retention, yield, and yield components of cotton grown with reduced stands of 20% to 40% from the uniform planting pattern of four seeds per 30.5 cm of row. Five field experiments were conducted from 2012-2014 using eight treatments arranged in a randomized complete design with six replications. Yield and yield component data were collected. The plant one-row skip one-row treatment resulted in significant yield losses across all five experiments compared to the uniform planting pattern. Treatments with 20% stand reductions did not result in lower total yields;however, each plant in these treatments had to produce two additional bolls to maintain yield. Treatments which had at least 61 cm skips, 40% stand reduction, resulted in lower yields. Treatments had minor affects on boll weight, and lint percentage. The uniform planting pattern produced 67% of its yield from position one bolls compared to about 50% for treatments with reduced stands. Reduced stand treatments produced about 20% of their yield on monopodial branches compared to 10% for the uniform treatment. With modern precision planting equipments, opportunities exist to reduce seed rate and maintain yield;however, many production risk factors must also be considered before a reduced seeding rate is adopted.

关键词： Cotton Plant Population Fruit Retention Plant Skips

Chromosome Substitution Lines:Useful Genomic Resources in Cotton

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棉花学报 2008年第S1期20卷 111-页

作者： SAHA Sukumar jenkins johnie N MCARTY Jack C STELLY David USDA-ARS Crop Science Research Laboratory P.O.Box 5367 Mississippi State Dept.Soil & Crop Sciences TAMU College Station

The genus Gossypium is a very diverse one with about 50 ***,a very narrow germplasm base is presently being used for genetic improvement of Upland *** wild

关键词： CS