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Back to wild relatives for future breeding through super-pangenome

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Molecular Plant 2023年第9期16卷 1363-1365页

作者： Ali Raza abhishek bohra Vanika Garg Rajeev K.Varshney College of Agriculture Fujian Agriculture and Forestry UniversityFuzhou 350002China WA State Agricultural Biotechnology Centre Centre for Crop and Food InnovationFood Futures InstituteMurdoch UniversityMurdochWA 6150Australia

Crop wild relatives(CWRs)deliver untapped genetic diversity,as they contain valuable breeding traits absent in the cultivated pool,e.g.,traits imparting climate *** genetic material from CWRs to breeding programs can advance effective traits and broaden the genetic base of cultivated crops(bohra et al.,2022).The availability of genetic diversity in crop breeding programs is important for accelerating crop production while safeguarding food safety and agricultural *** domestication and artificial selection have paved the way for crop cultivars tailored to evolving human requirements and modern cultivation ***,domestication and breeding have significantly reduced genetic diversity in modern crops(Khan et al.,2020;bohra et al.,2022).Owing to the extensive genetic and phenotypic variability,CWRs serve as valuable genetic reservoirs for crop improvement(bohra et al.,2022;Li et al.,2023).The use of CWRs in breeding programs is not that straightforward,as linkage drags often remain difficult to overcome.

关键词： breeding crops cultivated

Novel CMS lines in pigeonpea[Cajanus cajan(L.)Millspaugh]derived from cytoplasmic substitutions,and their effective restoration and deployment in hybrid breeding

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The Crop Journal 2017年第1期5卷 89-94页

作者： abhishek bohra Rintu Jha Indra Prakash Singh Gaurav Pandey Shalini Pareek Partha Sarathi Basu Sushil Kumar Chaturvedi Narendra Pratap Singh ICAR Indian Institute of Pulses Research(IIPR)Kanpur 208024India

The availability of stable cytoplasmic male sterile(CMS or A) lines coupled with a robust restoration system(R lines) is an essential prerequisite for efficient hybrid ***-enabled hybrid technology holds immense potential to enhance the long-stagnant productivity of pigeonpea. In the present investigation, cytoplasmic substitutions were made in the nuclear backgrounds of early-maturing pigeonpea varieties or lines. Three new CMS lines(ICPL 88039 A, Pusa 992 A, and DPP 3-2A) resulted from genetic crosses involving cytoplasmic donors from A2(GT 288A) and A4(ICPA 2089) categories. In addition to visual inspection of anthers, pollen-staining techniques and scanning electron microscopy(SEM)analysis were used to confirm pollen sterility. Further, given the relevance of the plant mitochondrial genome to CMS manifestation, 25 mitochondrion-specific DNA markers were assayed on these newly developed A lines and isogenic maintainer(B) lines. DNA polymorphism between Pusa 992 A and Pusa 992 B as revealed by the nad7a_del marker confirmed the successful combination of sterilizing cytoplasm(A4) and nonrestoring nuclear background(Pusa 992). Such cytoplasm-specific DNA markers are required for A2-CMS as well. Further, to assess restoration ability, potential restorers were crossed with these CMS lines, and as a consequence, promising A × R combinations exhibiting 100%pollen fertility could be identified. In parallel, we also analyzed the inheritance patterns underlying fertility restoration using ICPL 88039A-derived F2 and BC1F1populations,and established a monogenic dominant model to explain the phenomenon of A2-CMS restoration. In summary, we report the successful development of new CMS lines and describe their effective deployment in hybrid breeding of pigeonpea.

关键词： Cytoplasm Hybrid Mitochondria Pigeonpea Restorer Sterility

Fast integration and accumulation of beneficial breeding alleles through an AB–NAMIC strategy in wheat

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Plant Communications 2023年第3期4卷 66-79页

作者： Chengzhi Jiao Chenyang Hao Tian Li abhishek bohra Lanfen Wang Jian Hou Hongxia Liu Hong Liu Jing Zhao Yamei Wang Yunchuan Liu Zhiwei Wang Xin Jing Xiue Wang Rajeev K.Varshney Junjie Fu Xueyong Zhang The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences Chinese Academy of Agricultural SciencesBeijing 100081China State Key Laboratory of Crop Genetics and Germplasm Enhancement Cytogenetics InstituteNanjing Agricultural UniversityNanjingJiangsu 210095China Centre for Crop&Food Innovation WA State Agricultural Biotechnology CentreFood Futures InstituteMurdoch UniversityPerthWA 6150Australia Smartgenomics Technology Institute Tianjin 301700China

Wheat(Triticum aestivum)is among the most important staple crops for safeguarding the food security of the growing world *** bridge the gap between genebank diversity and breeding programs,we developed an advanced backcross-nested association mapping plus inter-crossed population(AB-NAMIC)by crossing three popular wheat cultivars as recurrent founders to 20 germplasm lines from a mini core *** backcrossing combined with selection against undesirable traits and extensive crossing within and between sub-populations created new opportunities to detect unknown genes and increase the frequency of beneficial alleles in the AB-NAMIC *** performed phenotyping of 590 AB-NAMIC lines and a natural panel of 476 cultivars for six consecutive growing seasons and genotyped these 1066 lines with a 660K SNP ***-wide association studies of both panels for plant development and yield traits demonstrated improved power to detect rare alleles and loci with medium genetic effects in ***,genome-wide association studies in AB-NAMIC detected the candidate gene TaSWEET6-7B(TraesCS7B03G1216700),which has high homology to the rice SWEET6b gene and exerts strong effects on adaptation and yield *** commercial release of two derived AB-NAMIC lines attests to its direct applicability in wheat *** information on genome-wide association studymapping,candidate genes,and their haplotypes for breeding traits are available through *** research provides an excellent framework for fast-tracking exploration and accumulation of beneficial alleles stored in genebanks.

关键词： wheat genebank AB-NAMIC genome-wide association studies GWAS beneficial alleles genomics-assisted breeding WheatGAB

A Comprehensive Transcriptome Assembly of Pigeonpea （Cajanus cajan L.） using Sanger and Second-Generation Sequencing Platforms

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Molecular Plant 2012年第5期5卷 1020-1028页

作者： Himabindu Kudapa Arvind K. Bharti Steven B. Cannon Andrew D. Farmer Benjamin Mulaosmanovi Robin Kramer abhishek bohra Nathan T. Weeks John A. Crow Reetu Tuteja Trushar Shah Sutapa Dutta Deepak K. Gupta Archana Singh Kishor Gaikwad Tilak R. Sharma Gregory D. May Nagendra K. Singh Rajeev K. Varshney International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) Patancheru 502324 india National Center for Genome Resources (NCGR) Santa Fe NM 87505 USA United States Department of Agriculture-Agricultural Research Service (USDA-ARS) Corn Insects and Crop Genetics Research Unit Ames IA USA National Research Centre on Plant Biotechnology (NRCPB) Indian Agricultural Research Institute New Delhi 110 012 India Department of Agronomy Iowa State University Amens IA USA CGIAR Generation Challenge Programme (GCP) c/o ClMMYT 06600 Mexico DF Mexico

A comprehensive transcriptome assembly for pigeonpea has been developed by analyzing 128.9 million short Illumina GA IIx single end reads, 2.19 million single end FLX/454 reads, and 18 353 Sanger expressed sequenced tags from more than 16 genotypes. The resultant transcriptome assembly, referred to as CcTA v2, comprised 21 434 transcript as- sembly contigs （TACs） with an N50 of 1510 bp, the largest one being -8 kb. Of the 21 434 TACs, 16 622 （77.5%） could be mapped on to the soybean genome build 1.0.9 under fairly stringent alignment parameters. Based on knowledge of intron junctions, 10 009 primer pairs were designed from 5033 TACs for amplifying intron spanning regions （ISRs）. By using in silico mapping of BAC-end-derived SSR loci of pigeonpea on the soybean genome as a reference, putative mapping posi- tions at the chromosome level were predicted for 6284 ISR markers, covering all 11 pigeonpea chromosomes. A subset of 128 ISR markers were analyzed on a set of eight genotypes. While 116 markers were validated, 70 markers showed one to three alleles, with an average of 0.16 polymorphism information content （PIC） value. In summary, the CcTA v2 transcript assembly and ISR markers will serve as a useful resource to accelerate genetic research and breeding applications in pigeonpea.

关键词： Cajanus cajan (L.) second-generation sequencing transcriptome assembly intron spanning region (ISR)markers.

A Survey of Fodder Plants in Mid-altitude Himalayan Rangelands of Uttarakhand,India

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Journal of Mountain Science 2008年第3期5卷 265-278页

作者： Vir Singh RD Gaur Babita bohra Professor Department of Environmental ScienceCollege of Basic Sciences and HumanitiesGB Pant University of Agriculture and TechnologyPantnagar-263145UttarakhandIndia Emeritus Professor Department of BotanyHNB Garhwal UniversitySrinagar-246174UttarakhandIndia Regional Rangeland Consultant International Centre for Integrated Mountain Development (ICIMOD)P.O. Box 3226KhumaltarKathmanduNepal

Himalayan rangelands, the crucial but by and large the neglected ecosystems, are an integral part of mountain farming systems. The present investigation is based on the extensive survey and collection of mid-altitude range plants from Almora and Champawat districts of Kumaun division in the Uttarakhand Himalaya in India, from September 2003 to June 2007. The rangelands studied were oak types, chirpine types, grass types and mixed ones. Some 300 species of grasses, other herbaceous plants, trees and shrubs were found in the mid-altitude rangelands. A sizeable number of species belonged to the family of Poaceae. The grass-dominated rangelands especially harboured a variety of grass species of good fodder value. The diversity of fodder plants is a proportion of the enormous biodiversity occurring in the parts of the Himalaya. A panorama of the biodiversity emerged in this study, which is of both intangible value and direct value for the livestock- and rangeland- dependent mountain communities, suggests a very high scope of the utilization of this natural and uncultivated biodiversity for supporting livestock- based livelihoods of the region. This biodiversity also has enormous bearing on the cultivated area of the region.

关键词： Rangelands mid-altitude fodder plants biodiversity Himalaya Uttarakhand

Chemical pre-treatments improve seed germination and seedling growth in Semecarpus kurzii:an ethnomedicinally important plant

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Journal of Forestry Research 2018年第5期29卷 1283-1289页

作者： Ajit Arun Waman Pooja bohra Avinash Norman Division of Horticulture and Forestry ICAR-Central Island Agricultural Research Institute

Semecarpus kurzii *** an important ethnomedicinal plant used for curing tumours,inflammation,fever and pain,and is also a source of iso ricinoleic *** the present investigation,effect of chemical pretreatments on germination and seedling growth revealed significant *** pre-treatments could improve germination and treatment with KNO_3 （9.9 mM）was significantly superior（94%） to the untreated control（76%）.Mean daily germination varied among the treatments（0.90–4.14 seeds per day）,when compared with 2.27 seeds per day in *** germination time was significantly reduced from 22.14 days（control） to 16.40 days（19.8 mM KNO_3） and 17.16 days（1.45 mM GA_3）.Treatment with KNO_3（19.8 mM） and GA_3（1.45 and 2.90 mM）significantly reduced the time for 50% *** with higher concentrations of GA_3 and KNO_3 exhibited significantly faster germination initiation（11.0 and 12.0 days,respectively） over the control（17.0 days）.Seedling vigour index was not improved by *** treatments did not improve shoot growth,collar thickness,or number of seedling leaves; however,root growth was significantly improved over *** with GA_3（2.90 mM） promoted leaf elongation but reduced leaf width *** with KNO_3 and GA_3 could be recommended to obtain healthy seedlings for establishing new plantations of this important medicinal plant species.

关键词： Conservation Indian system of medicines Tribal healthcare Wild cashew

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Intelligent Automation & Soft Computing 2023年第4期36卷 205-221页

作者： Navdeep bohra Vishal Bhatnagar Amit Choudhary Savita Ahlawat Dinesh Sheoran Ashish Kumari USICT GGSIPUNew Delhi110058India Maharaja Surajmal Institute of Technology New Delhi110058India NSUT East Campus(Formerly AIACTR)New Delhi110031India Maharaja Surajmal Institute New Delhi110058India

The traditional method of doing business has been disrupted by socialmedia. In order to develop the enterprise, it is essential to forecast the level ofinteraction that a new post would receive from social media users. It is possiblefor the user’s interest in any one social media post to be impacted by external factors or to dwindle as a result of changes in his behaviour. The popularity detectionstrategies that are user-based or population-based are unable to keep up with theseshifts, which leads to inaccurate forecasts. This work makes a prediction abouthow popular the post will be and addresses any anomalies caused by factors outside of the study. A novel improved PARAFAC (A-PARAFAC) method that istensor factorization-based has been presented in order to cope with the user criteria that will be used in the future to rate any project. We consolidated the information on the historically popular content, and we accelerated the computation bychoosing the top contents that were most like each other. The tensor is factorisedwith the application of the Adam optimization. It has been modified such that thebias is now included in the gradient function of A-PARAFAC, and the value ofthe bias is updated after each iteration. The prediction accuracy is improved by32.25% with this strategy compared to other state of the art methods.

关键词： Tensor decomposition popularity prediction group level popularity graphical clustering PARAFAC

Prognostic significance of hepatic encephalopathy in patients with cirrhosis treated with current standards of care

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World Journal of Gastroenterology 2020年第18期26卷 2221-2231页

作者： Anuj bohra Thomas Worland Samuel Hui Ryma Terbah Ann Farrell Marcus Robertson Department of Gastroenterology Monash HealthClayton 3168VictoriaAustralia Department of Gastroenterology Austin HealthHeidelberg 3084VictoriaAustralia Department of Medicine School of Clinical SciencesMonash UniversityClayton 3168VictoriaAustralia

BACKGROUND Hepatic encephalopathy(HE)is a reversible neuropsychiatric complication of liver cirrhosis and occurs in up to 50%of cirrhotic *** examining the prognostic significance of HE are limited despite the high prevalence in *** To define the clinical outcomes of patients after an episode of HE treated with current *** All patients hospitalised with HE requiring Rifaximin to 3 tertiary centres over46-mo(2012–2016)were identified via pharmacy dispensing *** with hepatocellular carcinoma and those prescribed Rifaximin prior to admission were *** records were reviewed to determine baseline characteristics and *** Kaplan-Meier method was used to calculate survival *** survival analysis was performed with variables reaching statistical significance included in a multivariate *** primary outcome was 12-mo mortality following commencement of ***188 patients were *** age was 57 years(IQR 50-65),71%were male and median model for end stage liver disease and Child Pugh scores were 25(IQR 18-31)and 11(IQR 9-12)*** most common causes of cirrhosis were alcohol(62%),hepatitis C(31%)and non-alcoholic fatty liver disease(20%).A precipitating cause for HE was found in 92%patients with infection(43%),GI bleeding(16%),medication non-compliance(15%)and electrolyte imbalance(14%)the most *** a mean follow up period of 12±13 mo 107(57%)patients died and 32(17%)received orthotopic liver *** common causes of death were decompensated chronic liver disease(57%)and sepsis(19%).The probability of survival was 44%and 35%at 12-and 24-mo *** multivariate analysis a model for end stage liver disease>15 and international normalised ratio reached statistical significance in predicting *** Despite advances made in the management of HE patients continue to have poor ***,in all patients

关键词： Hepatic encephalopathy Cirrhosis Portal hypertension Prognosis Rifaximin Lactulose

Transitioning patients with inflammatory bowel disease from hospital-based to rapid home-based infliximab: A stepwise, safety and patient-orientated process towards sustainability

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World Journal of Gastroenterology 2020年第36期26卷 5437-5449页

作者： Anuj bohra Qurat-Al-Ain Rizvi Charlotte Yuen Yu Keung Abhinav Vasudevan Daniel R van Langenberg Department of Gastroenterology Eastern HealthBox Hill 3128VictoriaAustralia Eastern Health Clinical School Monash UniversityBox Hill 3128VictoriaAustralia

BACKGROUND Infliximab and other intravenous biologic infusions are increasingly used for chronic disorders like inflammatory bowel disease(IBD).Rapid infliximab and home-based infusions are attractive solutions to address resource and capacity issues for infusion centres,yet infliximab infusion reactions reportedly occur in up to 25%of patients with IBD,even at the manufacturers’recommended infusion duration of 2 *** To evaluate the safety,cost and patient satisfaction of transitioning from hospitalbased,standard 2 h to rapid home-based,30-min infliximab *** All patients receiving rapid infliximab infusions for IBD between 2014 to 2017(39 mo)were compared with those who received standard two-hour IFX infusions between 2005-2013(96 mo)at a single IBD ***(per-infusion and perindividual)including adverse drug reactions(ADR),duration(based on needledeparture time)and other clinical data were extracted from electronic medical *** logistical regression analysis assessed factors potentially associated with increased risk of ADRs to rapid *** primary outcome was the safety[as per relative risk(RR)of (ADR)of(1)rapid 30 m infusions(both hospital-and home-based)vs standard 2 h infliximab ***,relative cost per infusion and patient satisfaction and productivity were evaluated in rapid infusion recipients who transitioned to home-based *** Of 129 patients who received 1461 rapid IFX infusions(2014-2017)were compared with 169 patients who received 2214 standard IFX infusions(2005-2013).Within the rapid cohort,55(42.6%)were males,median age 42 years(range 18,86),114(84%)had Crohn’s disease(CD)with a median disease duration 5 years(0,36).Median needle to departure time was higher in the standard than the rapid protocol group,108(70,253)vs 50(33,90)min,(P<0.001),with a per infusion cost of$AUD 107.50 vs$49.77,respectively(both P<0.001).There was no difference in median infusion duration or costs between rapi

关键词： Inflammatory bowel disease Infliximab Safety Cost Therapy Drug reaction