Next-generation sequencing technology: a boon to agriculture

Meena, Balakrishnan; Sharma, Tamanna; Purru, Supriya; Soam, S. K.; Rao, Ch. Srinivasa

doi:10.1007/s10722-022-01512-5

Cited by 7 publications

(4 citation statements)

References 123 publications

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“…Modern genetic tools are being used to gain a better understanding of which genes are responsible for specific traits in plants as well as to modify the genomes of plants to enhance their properties . The increased speed and lower costs of modern sequencing techniques is allowing plant scientists to determine the genomes of an increasing number of agriculturally important plants . This knowledge helps scientists improve their understanding of the role of specific genes or gene combinations on particular desirable or undesirable traits in plants, such as higher yields, improved resilience to environmental stresses, and enhanced nutritional profiles .…”

Section: Increasing Crop Yields Resilience and Nutritionmentioning

confidence: 99%

Designing a More Sustainable and Environmentally Friendly Food Supply: A Roadmap for Future Food and Agricultural Research

McClements

2024

ACS Sustainable Resour. Manage.

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There is an urgent need to change the way we produce, distribute, and consume foods due to several adverse effects the modern food supply is having on the environment, including greenhouse gas emissions, pollution, freshwater use, land use, and biodiversity loss. Concerted efforts are therefore required by food scientists around the world to generate the scientific knowledge and technological advances needed to develop a more sustainable global food supply chain. The purpose of this article is to highlight some of the most critical areas where research is needed to improve the sustainability and reduce the adverse environmental impact of food production. These areas include enhanced agricultural crops and livestock animals, improved fertilizers, pesticides, and antibiotics, reduced food and agricultural waste, conversion of waste streams into energy and valuable materials, alternative protein sources, and advanced food packaging materials, as well as many others. A range of advanced technologies is leading to important advances in many areas of food science and technology, including gene editing, nanotechnology, precision fermentation, biotechnology, and food architecture. An important objective of this article is to stimulate research and development in this important area so as to create a more sustainable and environmentally friendly global food supply system.

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Section: Increasing Crop Yields Resilience and Nutritionmentioning

confidence: 99%

Designing a More Sustainable and Environmentally Friendly Food Supply: A Roadmap for Future Food and Agricultural Research

McClements

2024

ACS Sustainable Resour. Manage.

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“…However, there is limited information available on this topic. Short reads and misassembly, which are disadvantages of NGS technology, quickly result in the loss of some vital information and greatly hinder its ability to estimate transcript abundance at a genome-wide scale [25,26].…”

Section: Introductionmentioning

confidence: 99%

De Novo Transcriptome Analysis by PacBio SMRT-Seq and Illumina RNA-Seq Provides New Insights into Polyphenol Biosynthesis in Chinese Olive Fruit

Ye,

Zhang,

Xie

et al. 2024

Horticulturae

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Polyphenols play a crucial role in fruit flavor. To elucidate the mechanism of fruit polyphenol metabolism, we constructed a transcriptome atlas through PacBio single-molecule real-time (SMRT) sequencing and Illumina next-generation sequencing (NGS) using Canarium album (Lour.) Raeusch., which is a fantastic fruit rich in polyphenolic compounds. In this work, PacBio full-length transcriptome assembly generated 135,439 isoforms with an average length of all isoforms of 2687.94 bp and an N50 length of 3224 bp. To gain deeper insights into the molecular mechanisms of polyphenol biosynthesis in C. album, we constructed twelve RNA-Seq libraries from four developmental stages of the fruits. We identified a total of 28,658 differentially expressed genes (DEGs). We found that many DEGs were involved in metabolic pathways, biosynthesis of secondary metabolites, biosynthesis of antibiotics, starch and sucrose metabolism, and plant hormone signal transduction. Here, we report the expression profiles of 215 DEGs encoding 27 enzymes involved in the polyphenol biosynthesis pathway in C. album. In addition, 285 differentially expressed transcription factors (TFs) continuously down-regulated in four developmental periods of C. album fruit, which may indicate their potential role in the response to polyphenol metabolism and phenylpropanoid biosynthesis pathways. This report will help us understand polyphenol biosynthesis’s functions and metabolic mechanism in C. album. The transcriptome data provide a valuable resource for genetic and genomics research. They will facilitate future work exploiting C. album and other fruits used as medicine and food.

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“…With the development of technologies [4][5][6][7][8] such as sequencing and gene editing, more and more genes and variants related to hair color have been mined and validated. The formation of wool color involves several processes, including the development of pigment cells, pigment synthesis, and pigment transport and distribution.…”

Section: Introductionmentioning

confidence: 99%

Selection signatures of wool color in Gangba sheep revealed by genome-wide SNP discovery

Zhang,

Luosang,

Yuan

et al. 2024

BMC Genomics

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Background Gangba sheep as a famous breed of Tibetan sheep, its wool color is mainly white and black. Gangba wool is economically important as a high-quality raw material for Tibetan blankets and Tibetan serge. However, relatively few studies have been conducted on the wool color of Tibetan sheep. Results To fill this research gap, this study conducted an in-depth analysis of two populations of Gangba sheep (black and white wool color) using whole genome resequencing to identify genetic variation associated with wool color. Utilizing PCA, Genetic Admixture, and N-J Tree analyses, the present study revealed a consistent genetic relationship and structure between black and white wool colored Gangba sheep populations, which is consistent with their breed history. Analysis of selection signatures using multiple methods (FST, π ratio, Tajima's D), 370 candidate genes were screened in the black wool group (GBB vs GBW); among them, MC1R, MLPH, SPIRE2, RAB17, SMARCA4, IRF4, CAV1, USP7, TP53, MYO6, MITF, MC2R, TET2, NF1, JAK1, GABRR1 genes are mainly associated with melanin synthesis, melanin delivery, and distribution. The enrichment results of the candidate genes identified 35 GO entries and 19 KEGG pathways associated with the formation of the black phenotype. 311 candidate genes were screened in the white wool group (GBW vs GBB); among them, REST, POU2F1, ADCY10, CCNB1, EP300, BRD4, GLI3, and SDHA genes were mainly associated with interfering with the differentiation of neural crest cells into melanocytes, affecting the proliferation of melanocytes, and inhibiting melanin synthesis. 31 GO entries and 22 KEGG pathways were associated with the formation of the white phenotype. Conclusions This study provides important information for understanding the genetic mechanism of wool color in Gangba, and provides genetic knowledge for improving and optimizing the wool color of Tibetan sheep. Genetic improvement and selective breeding to produce wool of specific colors can meet the demand for a diversity of wool products in the Tibetan wool textile market.

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Next-generation sequencing technology: a boon to agriculture

Cited by 7 publications

References 123 publications

Designing a More Sustainable and Environmentally Friendly Food Supply: A Roadmap for Future Food and Agricultural Research

Designing a More Sustainable and Environmentally Friendly Food Supply: A Roadmap for Future Food and Agricultural Research

De Novo Transcriptome Analysis by PacBio SMRT-Seq and Illumina RNA-Seq Provides New Insights into Polyphenol Biosynthesis in Chinese Olive Fruit

Selection signatures of wool color in Gangba sheep revealed by genome-wide SNP discovery

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