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糜子PmNAC1的克隆及生物信息学分析

山西农业科学 2023年第10期51卷 1162-1169页

作者：辛旭霞郑香然王海岗陈凌 santra dipak k 王瑞云乔治军山西农业大学农学院山西太谷030801 山西农业大学农业基因资源研究中心/农业农村部黄土高原作物基因资源与种质创制重点实验室/杂粮种质资源发掘与遗传改良山西省重点实验室山西太原030031 内布拉斯加大学林肯分校农艺系小宗粮豆研究与推广中心美国内布拉斯加州69361

糜子为禾本科草本植物,抗旱、耐盐碱、耐瘠、生育期短。为了给糜子抗逆分子育种提供候选基因,试验在前期转录组测序注释基因的基础上,利用糜子基因组染色体16上注释的NAC蛋白结构域比对得到PmNAC1基因的gDNA序列,通过PCR扩增、基因克隆... 详细信息

糜子为禾本科草本植物,抗旱、耐盐碱、耐瘠、生育期短。为了给糜子抗逆分子育种提供候选基因,试验在前期转录组测序注释基因的基础上,利用糜子基因组染色体16上注释的NAC蛋白结构域比对得到PmNAC1基因的gDNA序列,通过PCR扩增、基因克隆获得糜子的核苷酸序列,使用在线软件ORF Finder Blast对糜子NAC编码蛋白的理化特性及结构等进行生物信息学分析。结果表明,PmNAC1基因全长1 634 bp,编码423个氨基酸,无信号肽和跨膜结构;二级结构中氨基酸主要由8个α-螺旋和14个β-折叠组成,为亲水性蛋白,保守位点在第73~211位氨基酸,共有59个磷酸化位点;超出水平线0.5的是糖基化位点;构建了糜子转录因子NAC氨基酸序列系统发育进化树,PmNAC1蛋白与柳枝稷CUC2的亲缘关系最近,二者的遗传变异系数为0.06。

关键词：糜子 PmNAC1 克隆生物信息学分析

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山西糜黍遗传差异评估及分子身份证构建

山西农业科学 2023年第10期51卷 1178-1188页

作者：冯智尊杨雅斐王海岗陈凌 santra dipak k 王瑞云乔治军山西农业大学农学院山西太谷030801 山西农业大学农业基因资源研究中心/农业农村部黄土高原作物基因资源与种质创制重点实验室/杂粮种质资源发掘与遗传改良山西省重点实验室山西太原030031 内布拉斯加大学林肯分校农艺系小宗粮豆研究与推广中心美国内布拉斯加州69361

应用微卫星标记对糜黍资源进行遗传多样性分析,确定其遗传背景,有利于资源的合理高效利用。以80份山西糜黍核心种质为材料,44个SSR标记为检测工具,利用软件PowerMarker 3.25和PopGen 1.32计算遗传多样性衡量参数,使用MEGA 11.0.10软件... 详细信息

应用微卫星标记对糜黍资源进行遗传多样性分析,确定其遗传背景,有利于资源的合理高效利用。以80份山西糜黍核心种质为材料,44个SSR标记为检测工具,利用软件PowerMarker 3.25和PopGen 1.32计算遗传多样性衡量参数,使用MEGA 11.0.10软件绘制聚类图,使用NTSYSpc2.11a软件进行主成分分析,应用ID Analysis 4.0软件构建材料的DNA分子身份证。结果表明,80份材料在44个位点共检测出130个等位变异,平均每个位点检出3个;基于UPGMA聚类分析,80份材料划归4个类群(Ⅰ、Ⅱ、Ⅲ、Ⅳ),分别以晋中市、忻州市、朔州市、忻州市材料为主。主成分分析将材料划归10类(G1~G10),其中,G1均来自大同市,G2均来自朔州市,G3均来自忻州市,G4均来自太原市,G5~G10分别来自阳泉市、晋中市、吕梁市、长治市、临汾市和运城市。综合多态性信息含量(PIC)和Shannon多样性指数(I)值得出,高于平均值的SSR引物有21对(RYW3、RYW7、RYW11、RYW14、RYW18、RYW26、RYW28、RYW29、RYW30、RYW31、RYW37、RYW39、RYW40、RYW49、RYW54、RYW56、RYW61、RYW62、RYW65、RYW67和RYW82)。利用ID Analysis 4.0软件分析,发现16个SSR(RYW62、RYW67、RYW56、RYW65、RYW61、RYW40、RYW37、RYW31、RYW82、RYW29、RYW28、RYW49、RYW39、RYW54、RYW18和RYW30)组合在一起可区分全部材料。通过在线二维码生成器,对试验材料的基本信息及字符串信息进行加工处理,可得到二维码DNA分子身份证。

关键词：糜黍 SSR 遗传多样性 DNA分子身份证山西

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黍稷EST-SSR标记的开发

山西农业科学 2022年第7期50卷 927-937页

作者：商春悦王蓉王海岗陈凌 santra dipak k 乔治军王瑞云山西农业大学农学院山西太谷030801 山西农业大学农业基因资源研究中心/农业农村部黄土高原作物基因资源与种质创制重点实验室/杂粮种质资源发掘与遗传改良山西省重点实验室山西太原030031 内布拉斯加大学林肯分校农艺系小宗粮豆研究与推广中心美国内布拉斯加州69361

黍稷是起源于我国的古老作物之一,抗逆性强且遗传多样性丰富,EST-SSR已成为植物遗传多样性分析以及指纹图谱和遗传图谱构建的重要工具。选取来自黑龙江、陕西、内蒙古、青海、波兰以及印度共6个不同地理区域的黍稷为试验材料,以前期黄黍... 详细信息

黍稷是起源于我国的古老作物之一,抗逆性强且遗传多样性丰富,EST-SSR已成为植物遗传多样性分析以及指纹图谱和遗传图谱构建的重要工具。选取来自黑龙江、陕西、内蒙古、青海、波兰以及印度共6个不同地理区域的黍稷为试验材料,以前期黄黍稷(00005272)与镇原大黍稷转录测序结果选取114个EST-SSR三碱基重复标记,通过聚丙烯酰胺凝胶电泳筛选具有多态性的引物,利用PowerMarker 3.25和PopGen 1.32计算遗传多样性参数。结果表明,43对引物具有多态性(多态率为37.7%),43个EST-SSR标记的碱基重复类型有24种,GCG三核苷酸重复类型占12%。引物分辨率Rp值平均为2.09,其中,Rp值介于2.0~2.5的标记频次最多(15个),介于0~1.0标记频次最少(2个);Rp值平均为0.74。43个EST-SSR标记共有118个等位基因变异(平均2.744 2个),有效等位变异(Ne)为1.851 9~2.941 2(平均为2.401 1);多样性指数(Ⅰ)为0.562 3~1.098 6(平均为0.916 0);观测杂合度(Ho)为0.166 7~1.000 0(平均为0.549 2);期望观测杂合度(He)为0.428 6~0.750 0(平均为0.632 1);Nei’s期望杂合度(Nei)为0.375 0~0.666 7(平均为0.566 5);多态性信息含量(PIC)为0.239 2~0.810 2(平均为0.625 2),说明43对EST-SSR引物为高度多态性引物,可以用于栽培黍稷的指纹图谱构建和种质遗传多样性分析。

关键词：黍稷 EST-SSR 引物分辨率多态性信息含量多样性指数

Effect of Cold-Mediated Pretreatment on Microspore Culture in Winter and Spring Wheat

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American Journal of Plant Sciences 2013年第11期4卷 2259-2264页

作者： Rituraj khound Meenakshi santra P. Stephen Baenziger dipak k. santra Department of Agronomy and Horticulture University of Nebraska-Lincoln Lincoln USA Panhandle Research and Extension Center University of Nebraska-Lincoln Scottsbluff USA Soil and Crop Sciences Colorado State University Fort Collins USA

Microspore culture of wheat generates completely homozygous (doubled haploid) plants in a single generation thereby reducing the time required for wheat variety development. Success of microspore culture in spring wheat is relatively higher than that in winter wheat. Cold mediated pretreatment was reported to improve response of microspore culture in wheat. The objective of the study was to determine and compare the influence of cold pretreatment on microspore culture in spring and winter wheat. Three spring (“Chris”, “Express”, and “Macon”) and three winter (“Anton”, “Antelope”, and “Camelot”) wheat cultivars were used. In cold pretreatment, excised anthers were incubated in solution B at 25°C-28°C for 4-5 days followed by cold treatment at 4°C for 5 days and were compared with the no-cold pretreatment at 25°C-28°C for 4-5 days. Isolated microspores were cultured in induction medium (MMS4) at 27°C-28°C for 25-30 days in the dark. Embryos (1-2 mm size) were transferred to regeneration medium (MMS5). Numbers of multicellular structures, transferable embryos and green plants were counted and data were used for analysis of variance using a generalized linear model. It was observed that cold pretreatment increased multicellular structures, transferable embryos and green plants in both spring and winter wheat. However, the degree of improvement was higher in spring wheat compared to winter wheat. The cultivars within spring and winter wheat responded differently. Development of embryos from pro-embryos was 4-5 folds lower in winter wheat than that in spring wheat, indicating requirement of a possibly different hormonal composition in induction medium for improving embryo induction in winter wheat. This report may provide future direction of research to improve microspore culture response in winter wheat.

关键词： Androgenesis Doubled Haploid Homozygosity Biotechnology Breeding

Development and Characterization of SSR Markers in Proso Millet Based on Switchgrass Genomics

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American Journal of Plant Sciences 2014年第1期5卷 175-186页

作者： Santosh G. Rajput Tammy Plyler-Harveson dipak k. santra Panhandle Research and Extension Center University of Ne-braska-Lincoln Scottsbluff USA

Proso millet (Panicummiliaceum) has highwater use efficiency (WUE), a short growing-season, and is highly adapted to a semi-arid climate. Genomic resources for proso millet are very limited. Large numbers of DNA markers and other genomic tools in proso millet can readily be developed by using genomic resources in related grasses. The objectives of the present report were to 1) test and characterize switchgrass SSR markers for use in proso millet, and 2) elucidate repeat-motifs in proso millet based on new SSR marker analysis. A total of 548 SSR markers were tested on 8 proso millet genotypes. Out of these, 339 amplified SSR markers in proso millet. This showed that 62% of the switchgrass SSR markers were transferable to proso millet. Of these 339 markers, 254 were highly polymorphic among the 8 proso genotypes. The resolving power of these 254 polymorphic SSR markers ranged from 0.25-14.75 with an average of 2.71. The 254 polymorphic SSR markers amplified 984 alleles in the ranges of 50 bp to 1300 bp. The majority of the SSR markers (221 of 254) amplified dinucleotide repeats. Based on SSR marker analysis, AG/GA was the most abundant repeat-motifs in proso millet. Switchgrass genomic information seems to be the most useful for developing DNA markers in proso millet. Markers developed in this study will be helpful for linkage map construction, mapping agronomic traits and future molecular breeding efforts in proso millet.

关键词： Millet Minor Crops Comparative Genomics Molecular Breeding

Bioassay of Winter Wheat for Gibberellic Acid Sensitivity

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American Journal of Plant Sciences 2013年第10期4卷 2015-2022页

作者： Alexander D. Pavlista dipak k. santra David D. Baltensperger Department of Agronomy and Horticulture University of Nebraska Panhandle Research & Extension Center Scottsbluff USA Department of Soil and Crop Sciences Texas A&M University College Station USA.

Increasing winter wheat seedling growth would make it a better winter cover crop. Gibberellic acid (GA3) seed treatment may accomplish this by stimulating stem growth. A bioassay, mimicking field conditions, could determine the relative sensitivity of conventional and semi-dwarf cultivars. In growth chambers set for cool (10℃/4℃) and warm (21℃/4℃) conditions, wheat seeds were treated with 0 and 125 to 16,000 ppm GA3. The cultivars Goodstreak (tall or conventional) and Wesley (semi-dwarf) were compared as standards. Emergence and plant height were measured. “Goodstreak” showed a significant growth promotion at 500 ppm GA3 when seeds were dipped and 2000 ppm when GA3 was applied in-furrow under both temperature regimes. “Wesley” in general required the same or a higher dose of GA3. Separately, the seeds of nine other cultivars were treated with GA3 as the standards. Based on maximum height promotion, the most sensitive cultivars under cool conditions were Goodstreak, Harry, Millenium, and Wahoo;under warm conditions, the most sensitive cultivars were Alliance, Goodstreak, Jagalene, and Millenium. In general, the least GA3 sensitive cultivars were Arrowsmith, Scout66, and Wesley. “Buckskin” and “InfinityCL” were intermediate. The rye cultivar Rymin also was tested and showed less sensitivity to GA3 than “Goodstreak”. When 6 benzyladenine (6BA) with GA3 was applied to “Goodstreak” and “Wesley” seed, emergence, plant height and weight, and tiller formation were reduced. Wheat cultivars will respond to GA3 and differ in the amount of GA3 needed. The results of this growth chamber study will guide subsequent field trials.

关键词： Plant Growth Regulator Gibberellin Planting Aid Cover Crop

Gibberellic Acid Promotes Early Growth of Winter Wheat and Rye

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American Journal of Plant Sciences 2014年第20期5卷 2984-2996页

作者： Alexander D. Pavlista David D. Baltensperger dipak k. santra Gary W. Hergert Steve knox Department of Agronomy and Horticulture University of Nebraska Panhandle Research & Extension Center Scottsbluff NE USA Department of Soil and Crop Sciences Texas A&M University College Station TX USA Nebraska Crop Improvement Association Lincoln NE USA

Winter wheat (Triticum aestivum) planting in Nebraska is recommended for mid Sep but summer crops are often harvested around Oct 1. Also, weather may delay planting. Could gibberellic acid (GA3), a growth stimulant, overcome the delayed seedling growth from late planting? Irrigated field trials were planted from 2005 to 2010 applying GA3 to wheat seed of cvs. Goodstreak and Wesley. In 2005, dip, spray and furrow GA3 applications to seed were tested. Dip and spray gave similar results. Furrow application was calculated too costly. Further tests used seed dips. In 2006 to 2008 planting, wheat was planted about 15 Sep, 1 Oct and 15 Oct. Trials planted in 2007 and 2008 included winter rye (Secale cereale) cv. Rymin. Heights in mid Nov showed a reduction with later planting. When planted about 1 Oct and 15 Oct, the delayed growth of Goodstreak, compared to planting two weeks earlier, was fully overcome by GA3 at 250 ppm. For Wesley, 1000 ppm GA3 was needed to nearly overcome later planting. Rymin rye gave an intermediate response between the two wheat cultivars. Spring and summer heights were not affected by GA3. Spring biomass, yield and harvested seed germination showed no GA3 effect. In later trials (planted in 2009 and 2010), the cytokinin 6-benzyl adenine (6BA) was added to GA3 to stimulate tiller formation. In the 1st year, 6BA at 2000 ppm depressed height, weight and yield without tiller promotion. Repeating the trial with lower rates (31 - 125 ppm 6BA) did not offer an additional advantage to GA3. The results indicate that seed application of GA3 can overcome delayed growth resulting from delayed planting of winter wheat and rye under irrigation.

关键词： Plant Growth Regulator Gibberellin Planting Aid Wind Erosion Soil Erosion Cover Crop Crop Rotation

用微卫星标记分析北方春糜子区黍稷的遗传差异

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山西农业科学 2022年第4期50卷 494-503页

作者：段政勇邢志王海岗陈凌 dipak k santra 王瑞云乔治军山西农业大学农学院山西太谷030801 山西农业大学农业基因资源研究中心/农业农村部黄土高原作物基因资源与种质创制重点实验室/杂粮种质资源发掘与遗传改良山西省重点实验室山西太原030031 内布拉斯加大学林肯分校农艺系小宗粮豆研究与推广中心美国内布拉斯加州69361

利用80对高基元SSR引物检测北方春糜子区48份黍稷材料的多态性,用PowerMarker 3.25对多态性进行分析,用Structure 2.2对群体遗传结构进行分析,使用MEGA 5.0构建聚类图,通过PopGen 1.32进行等位基因、有效等位基因数和多样性指数的计算,... 详细信息

利用80对高基元SSR引物检测北方春糜子区48份黍稷材料的多态性,用PowerMarker 3.25对多态性进行分析,用Structure 2.2对群体遗传结构进行分析,使用MEGA 5.0构建聚类图,通过PopGen 1.32进行等位基因、有效等位基因数和多样性指数的计算,用NTSYSpc 2.11软件进行主成分分析。结果表明,80个标记在48份材料中检测到206个等位变异,每个位点检测到2~3个,平均2.575个;其中,产生2个变异的位点有34个,产生3个变异的位点有46个。80个位点多样性指数介于0.6655(RYW95)~1.0786(RYW166),平均为0.8608;80个位点PIC值介于0.1850(RYW151)~0.7062(RYW111),平均为0.4536。不同地区的黍稷种质间的遗传距离为0.0286~0.0456,遗传一致度为0.9555~0.9736。基于UPGMA聚类分析,48份黍稷分为3个类群,类群Ⅰ、Ⅱ和Ⅲ分别以青海、山西和内蒙古材料为主。Structure分析结果将参试材料分为4个群组,分别以青海、内蒙古、甘肃和山西材料为主。PCA主成分分析发现,第1类群试验材料均来自青海,第2类群试验材料均来自甘肃,第3类群试验材料均来自内蒙古,第4类群试验材料均来自山西。通过对北方春糜子区48份样本黍稷的遗传多样性、遗传距离和遗传一致性分析,发现青海省材料具有最丰富的遗传多样性和复杂的遗传背景。

关键词：黍稷高基元SSR 遗传多样性遗传结构聚类分析