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Evaluation.of Movin. Grid Adjustmen. (MGA) Method in.Field Variation.Con.rol

Open.Journ.l of Statistics 2024年第5期14卷 450-466页

作者： Jixian. Wu johnie n. jenkins Jack C. McCarty Gen.tics an. Sustain.ble Agriculture Research Un.t USDA-ARS Mississippi State MS USA

Spatial variation.is often.en.oun.ered when.large scale field trials are con.ucted which can.result in.biased estimation.or prediction.of treatmen. (i.e. gen.type) values. An.effective removal of spatial variation.is n.eded to en.ure un.iased estimation.or prediction.an. thus in.rease the accuracy of field data evaluation. A movin. grid adjustmen. (MGA) method, which was proposed by Techn.w, was evaluated through Mon.e Carlo simulation.for its statistical properties regardin. field spatial variation.con.rol. Our simulation.results showed that the MGA method can.effectively accoun. for field spatial variation.if it does exist;however, this method will n.t chan.e phen.type results if field spatial variation.does n.t exist. The MGA method was applied to a large-scale cotton.field trial data set with two represen.ative agron.mic traits: lin. yield (stron. field spatial pattern. an. lin. percen.age (n. field spatial pattern.. The results suggested that the MGA method was able to effectively separate the spatial variation.in.ludin. blockin. effects from ran.om error variation.for lin. yield while the adjusted data remain.d almost iden.ical to the origin.l phen.typic data. With application.of the MGA method, the estimated varian.e for residuals was sign.fican.ly reduced (62.2% decrease) for lin. yield while more gen.tic variation.(29.7% in.rease) was detected compared to the origin.l data an.lysis subject to the con.en.ion.l ran.omized complete block design.an.lysis. On.the other han., the results were almost iden.ical for lin. percen.age with an. without the application.of the MGA method. Therefore, the MGA method can.be a useful addition.to en.an.e data an.lysis when.field spatial pattern.exists.

关键词： Spatial Variation Lin.ar Mixed Model Approach Experimen.al Design Movin. Grid Adjustmen. Crop Trial

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Comparison.of REML an. MIn.UE for Estimated Varian.e Compon.n.s an. Predicted Ran.om Effects

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Open.Journ.l of Statistics 2016年第5期6卷 814-823页

作者： n.n.n.n.johnie n. jenkins Jack C. McCarty Jixian. Wu Departmen. of Mathematics an. Statistics South Dakota State Un.versity Brookings SD USA Crop Scien.e Research Laboratory USDA-ARS Mississippi State MS USA Agron.my Horticulture and Plant Science Department South Dakota State University Brookings SD USA

Lin.ar mixed model (LMM) approaches have been.widely applied in.man. areas of research data an.lysis because they offer great flexibility for differen. data structures an. lin.ar model systems. In.this study, emphasis is placed on.comparin. the properties of two LMM approaches: restricted maximum likelihood (REML) an. min.mum n.rm quadratic un.iased estimation.(MIn.UE) with an. without resamplin. techn.ques bein. in.luded. Bias, testin. power, Type I error, an. computin. time were compared between.REML an. MIn.UE approaches with an. without Jackkn.fe techn.que based on.500 simulated data sets. Results showed that MIn.UE an. REML methods performed equally regardin. bias, Type I error, an. power. Jackkn.fe-based MIn.UE an. REML greatly improved power compared to n.n.Jackkn.fe based lin.ar mixed model approaches. Results also showed that MIn.UE is more time-savin. compared to REML, especially with the use of resamplin. techn.ques an. large data set an.lysis. Results from the actual cotton.data an.lysis were in.agreemen. with our simulated results. Therefore, Jackkn.fe-based MIn.UE approaches could be recommen.ed to achieve desirable power with reduced time for a large data an.lysis an. model simulation..

关键词： Comparison.of REML an. MIn.UE for Estimated Varian.e Compon.n.s an. Predicted Ran.om Effects

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An.Adaptive Sequen.ial Replacemen. Method for Variable Selection.in.Lin.ar Regression.An.lysis

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Open.Journ.l of Statistics 2023年第5期13卷 746-760页

作者： Jixian. Wu johnie n. jenkins Jack C. McCarty Jr. Gen.tics an. Sustain.ble Agriculture Research Un.t USDA-ARS Mississippi State USA

With the rapid developmen. of Dn. techn.logies, high throughput gen.mic data have become a powerful leverage to locate desirable gen.tic loci associated with traits of importan.e in.various crop species. However, curren. gen.tic association.mappin. an.lyses are focused on.iden.ifyin. in.ividual QTLs. This study aimed to iden.ify a set of QTLs or gen.tic markers, which can.capture gen.tic variability for marker-assisted selection. Selectin. a set with k loci that can.maximize gen.tic variation.out of high throughput gen.mic data is a challen.in. issue. In.this study, we proposed an.adaptive sequen.ial replacemen. (ASR) method, which is con.idered a varian. of the sequen.ial replacemen. (SR) method. Through Mon.e Carlo simulation.an. comparin. with four other selection.methods: exhaustive, SR method, forward, an. backward methods we foun. that the ASR method sustain. con.isten. an. repeatable results comparable to the exhaustive method with much reduced computation.l in.en.ity.

关键词： Adaptive Sequen.ial Replacemen. Association.Mappin. Exhaustive Method Global Optimal Solution Sequen.ial Replacemen. Variable Selection

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Characterization.of a n.vel RIn.-Type Ubiquitin.E3 Ligase GhRIn.2 Differen.ially Expressed in.Cotton.Fiber

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American.Journ.l of Plan. Scien.es 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 Departmen. of Biochemistry Molecular Biology Entomology and Plant Pa-thology Mississippi State University Mississippi State USA In.titute for Gen.mics Biocomputing & Biotechnology Mississippi State Uni-versity Mississippi State USA Crop Scien.e Research Laboratory Agricultural Research Service United States Department of Agriculture Mississippi State USA Departmen. of Plan. an. Soil Scien.es Mississippi State University Mississippi State USA

The ubiquitin.proteasome proteolysis pathway is respon.ible for the degradation.of abn.rmal an. short-lived protein. to regulate man. importan. biochemical activities in.eukaryotes. By employin. affymetrix microarray an.lysis, we have iden.ified a n.vel ubiquitin.ligase E3 gen. GhRIn.2 that is differen.ially expressed between.two Gossypium hirsutum lin.s-Texas Marker-1 (TM-1) an. Chromosome Substitution.Lin. CS-B25. The CS-B25 lin. has chromosome 25 from G. barbaden.e substituted in.o TM-1. The complete n.cleotide sequen.es of GhRIn.2 alon. with its 5’-flan.in. region.were obtain.d by gen.mic walkin.. GhRIn.2 was highly expressed in.elon.atin. fiber, an. GUS expression.directed by the GhRIn.2 promoter was foun. in.hypocotyls an. youn. stems of tran.gen.c Arabidopsis plan.s. Usin. a yeast two-hybrid assay GhRIn.2 was foun. to in.eract with a PROTODERMAL FACTOR1 (GhPDF1) protein. GhPDF1 was expressed preferen.ially in.immature ovules an. fiber in.tials, an. the GhPDF1 gen. had been.suggested to play a role in.cell fate determin.tion.an. fiber developmen.. Pull down.an. plasmid swap assays further con.irmed the in.eraction.between.GhRIn.2 an. GhPDF1. The expression.an. protein.in.eraction.data in.icate that GhRIn.2 may be in.olved in.the turn.ver of GhPDF1 an. participation.in.the tran.ition.from in.tiation.to elon.ation.stages durin. fiber developmen.. Our data stron.ly suggest that the ubiquitin.proteasome pathway may regulate cotton.fiber growth an. developmen.. The n.cleotide sequen.e data of GhRIn.2 in.this article have been.submitted to the Gen.Ban. n.cleotide Sequen.e Data Bases un.er the accession.n.mber Ban.It 1,742,008 SeqKM 108,000.

关键词： Cotton Fiber Gossypium hirsutum G. barbaden.e RIn.-Type Ubiquitin Ligase Ubiquitin.tion

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Effectiven.ss of Combin.d Biochar an. Lign.te with Poultry Litter on.Soil Carbon.Sequestration.an. Soil Health

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Open.Journ.l of Soil Scien.e 2023年第2期13卷 124-149页

作者： Ardeshir Adeli John.P. Brooks Dan. Miles Todd Mlsn. Read Quen.in.johnie n. jenkins USDA-ARS Mississippi USA Mississippi State Un.versity Mississippi USA USDA-ARS-SEA Genetics and Sustainable Agricultural Research Unit Mississippi USA

Healthy soils are importan. to en.ure satisfactory crop growth an. yield. Poultry litter (PL), as an.organ.c fertilizer, has proven.to supply the soil with essen.ial macro an. micron.trien.s, en.an.e soil fertility, an. improve crop productivity. In.egratin. this treatmen. has the poten.ial to improve soil physical an. biological properties by in.reasin. soil carbon. C. However, rapid decomposition.an. min.ralization.of PL, particularly in.the hot an. humid southeastern.U.S., resulted in.losin. C an. reduced its effect on.soil health. Biochar an. lign.te have been.proposed to stabilize an. mitigate C loss through application.of fresh man.re. However, their combin.d effects with PL on.C sequestration.an. soil health compon.n.s are limited. A field experimen. was con.ucted on.Leeper silty clay loam soil from 2017 to 2020 to evaluate the combin.d effect on.soil properties when.applyin. biochar an. lign.te with PL to cotton.(Gossypium hirsutum L.). The experimen.al design.was a ran.omized complete block in.olvin. n.n. treatmen.s replicated three times. Treatmen.s in.luded PL an. in.rgan.c n.trogen. n. fertilizer with or without biochar an. lign.te, an. an.un.ertilized con.rol. Application.rates were 6.7 Mgkg⋅ha−1 for PL, 6.7 Mgkg⋅ha−1 for biochar an. lign.te an. 134 kg⋅ha−1 for in.rgan.c n.fertilizer. In.egration.of PL an. in.rgan.c fertilizer with biochar an. lign.te, resulted in.greater soil in.iltration. aggregate stability, plan. available water, reduced bulk den.ity an. pen.tration.resistan.e as compared to the sole application. of PL an. in.rgan.c fertilizer.

关键词： Soil Health Lign.te Biochar Poultry Litter

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Effects of Plan. Den.ity on.Boll Reten.ion.an. Yield of Cotton.in.the Mid-South

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American.Journ.l of Plan. Scien.es 2017年第4期8卷 891-906页

作者： Jack C. McCarty johnie n. jenkins Russell W. Hayes Martin.J. Wubben Gen.tics an. Sustain.ble Agriculture Research Un.t Crop Science Research Laboratory USDA-ARS Starkville MS USA

The n.mber of cotton.(Gossypium hirsutum L.) plan.s bein. grown.per un.t of lan. area has gain.d atten.ion.due to the techn.logy fees associated with seed con.ain.n. value added traits. We in.estigated boll reten.ion. yield, an. yield compon.n.s of cotton.grown.with reduced stan.s of 20% to 40% from the un.form plan.in. pattern.of four seeds per 30.5 cm of row. Five field experimen.s were con.ucted from 2012-2014 usin. eight treatmen.s arran.ed in.a ran.omized complete design.with six replication.. Yield an. yield compon.n. data were collected. The plan. on.-row skip on.-row treatmen. resulted in.sign.fican. yield losses across all five experimen.s compared to the un.form plan.in. pattern. Treatmen.s with 20% stan. reduction. did n.t result in.lower total yields;however, each plan. in.these treatmen.s had to produce two addition.l bolls to main.ain.yield. Treatmen.s which had at least 61 cm skips, 40% stan. reduction. resulted in.lower yields. Treatmen.s had min.r affects on.boll weight, an. lin. percen.age. The un.form plan.in. pattern.produced 67% of its yield from position.on. bolls compared to about 50% for treatmen.s with reduced stan.s. Reduced stan. treatmen.s produced about 20% of their yield on.mon.podial bran.hes compared to 10% for the un.form treatmen.. With modern.precision.plan.in. equipmen.s, opportun.ties exist to reduce seed rate an. main.ain.yield;however, man. production.risk factors must also be con.idered before a reduced seedin. rate is adopted.

关键词： Cotton Plan. Population Fruit Reten.ion Plan. Skips

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Tran.criptome An.lysis of Ten.DPA Fiber in.an.Uplan. Cotton.(<i>Gossypium hirsutum</i>) Lin. with Improved Fiber Traits from Phytochrome A1 Rn.i Plan.s

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American.Journ.l of Plan. Scien.es 2017年第10期8卷 2530-2553页

作者： Qin. Miao Pen. Den. Sukumar Saha johnie n. jenkins Chuan.Yu Hsu Ibrokhim Y. Abdurakhmon.v Zabardast T. Buriev Alan.Pepper Din.Pow Ma Departmen. of Biochemistry Molecular Biology Entomology and Plant Pathology Mississippi State University Mississippi State MS USA Departmen. of Pharmacology Weill Cornell Medical College New York NY USA USDA-ARS Crop Science Research Laboratory Mississippi State MS USA In.titute for Gen.mics Biocomputing and Biotechnology Mississippi State University Mississippi State MS USA Cen.er of Gen.mics an. Bioin.ormatics Academy of Sciences of Uzbekistan Tashkent Uzbekistan Departmen. of Biology Texas A & M University College Station TX USA

Silen.in. phytochrome A1 gen. (PHYA1) by Rn. in.erferen.e in.Uplan. cotton.(Gossypium hirsutum L. cv. Coker 312) had gen.rated PHYA1 Rn.i lin.s with improved fiber quality (lon.er, stron.er an. fin.r fiber). To reveal molecular mechan.sms that govern.fiber developmen. with positive fiber traits, a study of global gen. expression.profilin. of 10-DPA fibers in.a PHYA1 Rn.i lin. an. its paren. Coker 312 was con.ucted by high-throughput Rn. sequen.in.. A comparative an.lysis of tran.criptomes between.the two lin.s had iden.ified 142 gen.s that were differen.ially expressed in.the 10-DPA fiber of the Rn.i lin.. Gen. On.ology an.lysis showed that these differen.ially expressed gen.s were main.y in.olved in.metabolic pathways, heterocyclic/organ.c cyclic compoun. bin.in. an. multiple en.yme activities, an. cell structures which were reported to play importan. roles in.fiber developmen.. Twen.y-eight KEGG pathways were mapped for the 142 gen.s, an. the pathways related to glycolysis/glucon.ogen.sis an. pyruvate metabolism were the most abun.an. an. followed by cytochrome P450-in.olved pathways, suggestin. that fiber improvemen. could be through the regulation.of protein. in.olved in.cytochrome P450 pathways. Gen.s en.odin. WRKY tran.cription.factors, sucrose syn.hase, xyloglucan.en.otran.glucosylase hydrolase, udp-glucuron.te: xylan.alpha-glucuron.syltran.ferase, an. gen.s in.olved in.lipid metabolism an. ABA/brassin.steroid sign.l tran.duction.pathways were foun. differen.ially expressed in.the Rn.i lin.. These gen.s have direct impacts on.cotton.fiber quality. The results of this study elucidate molecular sign.tures an. possible mechan.sms of fiber improvemen. in.the backgroun. of PHYA1 Rn.i in.cotton.an. should help for future fin.-tun.n. an. programmin. of cotton.fiber developmen..

关键词： Fiber Developmen. Phytochrome A1 Rn. In.erferen.e Rn.-Seq Tran.criptome

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Tran.criptome An.lysis of Ten.Days Post An.hesis Elon.atin. Fiber in.the Uplan. Cotton.(<i>Gossypium hirsutum</i>) Chromosome Substitution.Lin. CS-B25

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American.Journ.l of Plan. Scien.es 2018年第6期9卷 1334-1361页

作者： Chuan.Yu Hsu Mark A. Arick II Qin. Miao Sukumar Saha johnie n. jenkins Mirzakamol S. Ayubov Ibrokhim Y. Abdurakhmon.v Dan.el G. Peterson.Din.Pow Ma In.titute for Gen.mics Biocomputing & Biotechnology Mississippi State University Mississippi State MS USA Departmen. of Biochemistry Molecular Biology Entomology and Plant Pathology Mississippi State University Mississippi State MS USA Departmen. of Pharmacology Weill Cornell Medical College Cornell University New York NY USA USDA-ARS Crop Science Research Laboratory Mississippi State MS USA Cen.er of Gen.mics an. Bioin.ormatics Academy Sciences of Uzbekistan Tashkent Uzbekistan

A chromosome substitution.lin., CS-B25, was developed by the substitution.of chromosome pair 25 of Gossypium hirsutum TM-1 with the homologous pair of chromosome 25 from G. barbaden.e, a double haploid Pima 3-79 lin.. CS-B25 has improved fiber traits compared to its paren. TM-1. To explore the molecule mechan.sms un.erlyin. improved fiber traits, deep sequen.in. of total Rn. was used to compare gen. expression.in.fibers of CS-B25 an. TM-1 at 10 days post an.hesis (10-DPA). A total of 1872 differen.ially expressed gen.s (DEGs) were detected between.the two lin.s, with 1175 up-regulated an. 697 down.regulated in.CS-B25. Gen. On.ology (GO) en.ichmen. an.lysis of the expression.data by Gen.rally Applicable Gen.-set En.ichmen. (GAGE) an. ReviGO in.icated that the most prevalen. Biological Process GO terms associated with DEGs in.luded Dn.-templated tran.cription. respon.e to oxidative stress, an. cellulose biosyn.hesis. En.iched Molecular Fun.tion.GO terms in.luded structural con.tituen.s of cytoskeleton. peroxidase activity, cellulose syn.hase (UDP-formin.) activity, an. tran.cription.regulatory region.sequen.e-specific Dn. bin.in. factors. GAGE was also used to fin. en.iched KEGG pathways, an. the highly represen.ed pathways were Biosyn.hesis of Amin. Acids, Starch an. Sucrose Metabolism, Phen.lpropan.id Biosyn.hesis, Protein.Processin. in.En.oplasmic Reticulum, an. Plan. Hormon. Sign.l Tran.duction. Man. of the iden.ified DEGs are in.olved in.cytoskeleton.an. cell wall metabolism. The results of gen. expression.data have provided n.w in.ight in.o the molecular mechan.sms of fiber developmen. durin. the fiber elon.ation.stage an. would offer n.vel can.idate gen.s that may be utilized in.cotton.fiber quality improvemen..

关键词： Chromosome Substitution Lin.s Differen.ially Expressed Gen.s Fiber Developmen. Quan.itative Real-Time PCR Rn. Sequen.in. Uplan. Cotton

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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 Gen.tica Sin.ca 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

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Con.tructin. Molecular Marker Lin.age Maps of Chromosome 14Sh an. 22Sh an. QTL Mappin. for Major Traits by Use of Substitution.Lin.s 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 Scien.e Research Laboratory Mississippi State

CSB14Sh,which is isogen.c for its recurren. paren. TM-1 except for chromosome 14 short arm,was crossed with TM-1,an. the F2 population.was produced.A total of 3800 SSR primer pairs coverin. the whole gen.me were used ... 详细信息

关键词： QTLs Con.tructin. Molecular Marker Lin.age Maps of Chromosome 14Sh an. 22Sh an. QTL Mappin. for Major Traits by Use of Substitution.Lin.s of Gossypium hirsutum L

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