Digital applications and artificial intelligence in agriculture toward next-generation plant phenotyping DOI
Pasquale Tripodi,

Nicola Nicastro,

Catello Pane

et al.

Crop and Pasture Science, Journal Year: 2022, Volume and Issue: 74(6), P. 597 - 614

Published: Feb. 1, 2022

In the upcoming years, global changes in agricultural and environmental systems will require innovative approaches crop research to ensure more efficient use of natural resources food security. Cutting-edge technologies for precision agriculture are fundamental improve a non-invasive manner, efficiency detection parameters, assess complex traits plants with high accuracy. The application sensing devices implementation strategies artificial intelligence acquisition management high-dimensional data play key role address needs next-generation boosting breeding crops. To that end, closing gap knowledge from other ‘omics’ sciences is primary objective relieve bottleneck still hinders potential thousands accessions existing each crop. Although it an emerging discipline, phenomics does not rely only on technological advances but embraces several scientific fields including biology, statistics bioinformatics. Therefore, establishing synergies among groups transnational efforts able facilitate access new computational methodologies related information community, needed. this review, we illustrate main concepts plant phenotyping along mechanisms underpinning imaging analysis both controlled environments open fields. We then describe machine learning their implication breeding, highlighting ongoing toward big-data management.

Language: Английский

Ensembl variation resources DOI Creative Commons
Sarah Hunt, William McLaren, Laurent Gil

et al.

Database, Journal Year: 2018, Volume and Issue: 2018

Published: Jan. 1, 2018

The major goal of sequencing humans and many other species is to understand the link between genomic variation, phenotype disease. There are numerous valuable well-established variation resources, but collating making sense non-homogeneous, often large-scale data sets from disparate sources remains a challenge. Without systematic catalogue these appropriate query annotation tools, understanding genome sequence an individual assessing their disease risk impossible. In Ensembl, we substantially solve this problem: develop methods facilitate integration broad access; aggregate information in consistent manner make it available variety standard formats, both visually programmatically; build analysis pipelines compare variants comprehensive sets; all tools publicly available.

Language: Английский

Citations

453
Crop Breeding Chips and Genotyping Platforms: Progress, Challenges, and Perspectives DOI Creative Commons
Awais Rasheed, Yuanfeng Hao, Xianchun Xia

et al.

Molecular Plant, Journal Year: 2017, Volume and Issue: 10(8), P. 1047 - 1064

Published: June 29, 2017

Language: Английский

Citations

435
Accelerating crop genetic gains with genomic selection DOI
Kai P. Voss‐Fels, Mark Cooper, Ben J. Hayes

et al.

Theoretical and Applied Genetics, Journal Year: 2018, Volume and Issue: 132(3), P. 669 - 686

Published: Dec. 19, 2018

Language: Английский

Citations

287
The Wheat 660K SNP array demonstrates great potential for marker‐assisted selection in polyploid wheat DOI Creative Commons

Congwei Sun,

Zhongdong Dong, Lei Zhao

et al.

Plant Biotechnology Journal, Journal Year: 2020, Volume and Issue: 18(6), P. 1354 - 1360

Published: Feb. 17, 2020

Abstract The rapid development and application of molecular marker assays have facilitated genomic selection genome‐wide linkage association studies in wheat breeding. Although PCR‐based markers (e.g. simple sequence repeats functional markers) genotyping by sequencing contributed greatly to gene discovery marker‐assisted selection, the release a more accurate complete bread reference genome has resulted design single‐nucleotide polymorphism (SNP) arrays based on different densities or targets. Here, we evaluated seven types SNP terms their number, distribution, density, associated genes, heterozygosity application. results suggested that Wheat 660K array contained highest percentage (99.05%) genome‐specific SNPs with reliable physical positions. density analysis indicated were almost evenly distributed across whole genome. In addition, 229 266 located 66 834 annotated promoter intervals. genes revealed covered all 35K (97.44%), 55K (99.73%), 90K (86.9%) 820K (85.3%) arrays. Therefore, could act as substitute for other 6 shows promise wide range possible applications. summary, is cost‐effective may be best choice targeted genetic improvement.

Language: Английский

Citations

228
Enhancing Genetic Gain through Genomic Selection: From Livestock to Plants DOI Creative Commons
Yunbi Xu, Xiaogang Liu, Junjie Fu

et al.

Plant Communications, Journal Year: 2019, Volume and Issue: 1(1), P. 100005 - 100005

Published: Oct. 17, 2019

Although long-term genetic gain has been achieved through increasing use of modern breeding methods and technologies, the rate needs to be accelerated meet humanity's demand for agricultural products. In this regard, genomic selection (GS) considered most promising improvement complex traits controlled by many genes each with minor effects. Livestock scientists pioneered GS application largely due livestock's significantly higher individual values greater reduction in generation interval that can GS. Large-scale plants refining field management improve heritability estimation prediction accuracy developing optimum models consideration genotype-by-environment interaction non-additive effects, along significant cost reduction. Moreover, it would more effective integrate other tools platforms accelerating process thereby further enhancing gain. addition, establishing an open-source network transdisciplinary approaches essential efficiency small- medium-sized enterprises research systems countries. New strategies centered on need developed.

Language: Английский

Citations

212
Next-Generation Sequencing Accelerates Crop Gene Discovery DOI
Khanh Nguyen, Alexandre Grondin, Brigitte Courtois

et al.

Trends in Plant Science, Journal Year: 2018, Volume and Issue: 24(3), P. 263 - 274

Published: Dec. 17, 2018

Language: Английский

Citations

142
From markers to genome-based breeding in wheat DOI
Awais Rasheed, Xianchun Xia

Theoretical and Applied Genetics, Journal Year: 2019, Volume and Issue: 132(3), P. 767 - 784

Published: Jan. 23, 2019

Language: Английский

Citations

121
Gene Networks Underlying Cannabinoid and Terpenoid Accumulation in Cannabis DOI Creative Commons
Jordan J. Zager, Iris Lange, Narayanan Srividya

et al.

PLANT PHYSIOLOGY, Journal Year: 2019, Volume and Issue: 180(4), P. 1877 - 1897

Published: May 28, 2019

Glandular trichomes are specialized anatomical structures that accumulate secretions with important biological roles in plant-environment interactions. These also have commercial uses the flavor, fragrance, and pharmaceutical industries. The capitate-stalked glandular of Cannabis sativa (cannabis), situated on surfaces bracts female flowers, primary site for biosynthesis storage resins rich cannabinoids terpenoids. In this study, we profiled nine cannabis strains purportedly different attributes, such as taste, color, smell, genetic origin. were isolated from each these strains, cell type-specific transcriptome data sets acquired. Cannabinoids terpenoids quantified flower buds. Statistical analyses indicated enable high-resolution differentiation by providing complementary information. Integrative revealed a coexpression network genes involved both imported precursors. Terpene synthase major monoterpenes sesquiterpenes routinely assayed testing laboratories identified functionally evaluated. addition to cloning variants previously characterized genes, specifically CsTPS14CT [(−)-limonene synthase] CsTPS15CT (β-myrcene synthase), evaluated encode enzymes activities not described cannabis, namely CsTPS18VF CsTPS19BL (nerolidol/linalool synthases), CsTPS16CC (germacrene B CsTPS20CT (hedycaryol synthase). This study lays groundwork developing better understanding complex chemistry biochemistry underlying resin accumulation across strains.

Language: Английский

Citations

121
Genotyping-by-Sequencing Derived High-Density Linkage Map and its Application to QTL Mapping of Flag Leaf Traits in Bread Wheat DOI Creative Commons
Waseem Hussain,

P. Stephen Baenziger,

Vikas Belamkar

et al.

Scientific Reports, Journal Year: 2017, Volume and Issue: 7(1)

Published: Nov. 21, 2017

Winter wheat parents 'Harry' (drought tolerant) and 'Wesley' susceptible) were used to develop a recombinant inbred population with future goals of identifying genomic regions associated drought tolerance. To precisely map regions, high-density linkage maps are prerequisite. In this study genotyping-by- sequencing (GBS) was construct the map. The contained 3,641 markers distributed on 21 chromosomes spanned 1,959 cM an average distance 1.8 between markers. constructed revealed strong collinearity in marker order across POPSEQ-v2.0, which based reliability for QTL mapping demonstrated by co-localizing genes previously mapped two highly heritable traits, chaff color, leaf cuticular wax. Applicability three quantitative flag length, width, area, identified QTLs four environments, expression varied environments. Two major stable QTLs, one each length (Qfll.hww-7A) width (Qflw.hww-5A) identified. will facilitate fine map-based cloning, comparative mapping, marker-assisted breeding endeavors.

Language: Английский

Citations

120
Development and Applications of a High Throughput Genotyping Tool for Polyploid Crops: Single Nucleotide Polymorphism (SNP) Array DOI Creative Commons
Qian You, Xiping Yang, Ze Peng

et al.

Frontiers in Plant Science, Journal Year: 2018, Volume and Issue: 9

Published: Feb. 6, 2018

Polypoid species play significant roles in agriculture and food production. Many crop are polyploid, such as potato, wheat, strawberry, sugarcane. Genotyping has been a daunting task for genetic studies of polyploid crops, which lags far behind the diploid species. Single nucleotide polymorphism (SNP) array is considered to be one of, high-throughput, relatively cost-efficient automated genotyping approaches. However, there challenges SNP identification complex, genomes, seriously slowed discovery development Ploidy factor impacting qualities validation rates markers arrays, proven very important tool molecular breeding. In this review, we 1) discussed pros cons general high throughput genotyping, 2) presented solutions calling species, 3) summarized selection criteria considerations design 4) illustrated applications several different then 5) challenges, available software, their accuracy comparisons genotype based on data polyploids, finally 6) provided series recommendations. This review presents complete overview polypoid will benefit research breeding genetics crops with complex genomes.

Language: Английский

Citations

109