Harnessing Knowledge from Maize and Rice Domestication for New Crop Breeding

Chen, Qiuyue; Li, Weiya; Tan, Lubin; Tian, Feng

doi:10.1016/j.molp.2020.12.006

Cited by 68 publications

(43 citation statements)

References 196 publications

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“…In the process of crop domestication, human beings have paid particular attention to yield, shelf-life, and resistance to biotic stresses [ 7 , 39 ], especially seed and fruit development, but human have different perference for different species. It seems that people are inclined to select larger seeds to improve the emergence rate, yield, quality, and other important traits, especially in edible seed crops such as rapeseed [ 40 ] and bean [ 41 ].…”

Section: Discussionmentioning

confidence: 99%

A high-continuity and annotated tomato reference genome

Wang

Geng

et al. 2021

BMC Genomics

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Background Genetic and functional genomics studies require a high-quality genome assembly. Tomato (Solanum lycopersicum), an important horticultural crop, is an ideal model species for the study of fruit development. Results Here, we assembled an updated reference genome of S. lycopersicum cv. Heinz 1706 that was 799.09 Mb in length, containing 34,384 predicted protein-coding genes and 65.66% repetitive sequences. By comparing the genomes of S. lycopersicum and S. pimpinellifolium LA2093, we found a large number of genomic fragments probably associated with human selection, which may have had crucial roles in the domestication of tomato. We also used a recombinant inbred line (RIL) population to generate a high-density genetic map with high resolution and accuracy. Using these resources, we identified a number of candidate genes that were likely to be related to important agronomic traits in tomato. Conclusion Our results offer opportunities for understanding the evolution of the tomato genome and will facilitate the study of genetic mechanisms in tomato biology.

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Section: Discussionmentioning

confidence: 99%

A high-continuity and annotated tomato reference genome

Wang

Geng

et al. 2021

BMC Genomics

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“…Throughout history, the basic principle behind the efficient domestication and improvement of crops has been to select plants based upon their phenotypes. [ 47 ]. People will select for preferred traits in their crops.…”

Section: Discussionmentioning

confidence: 99%

Transcriptome and Resequencing Analyses Provide Insight into Differences in Organic Acid Accumulation in Two Pear Varieties

Qiao

Jia

et al. 2021

IJMS

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Fruit acidity is one of the main determinants of fruit flavor and a target trait in fruit breeding. However, the genomic mechanisms governing acidity variation among different pear varieties remain poorly understood. In this study, two pear varieties with contrasting organic acid levels, ‘Dangshansuli’ (low-acidity) and ‘Amute’ (high-acidity), were selected, and a combination of transcriptome and population genomics analyses were applied to characterize their patterns of gene expression and genetic variation. Based on RNA-seq data analysis, differentially expressed genes (DEGs) involved in organic acid metabolism and accumulation were identified. Weighted correlation network analysis (WGCNA) revealed that nine candidate TCA (tricarboxylic acid)-related DEGs and three acid transporter-related DEGs were located in three key modules. The regulatory networks of the above candidate genes were also predicted. By integrating pear resequencing data, two domestication-related genes were found to be upregulated in ‘Amute’, and this trend was further validated for other pear varieties with high levels of organic acid, suggesting distinct selective sweeps during pear dissemination and domestication. Collectively, this study provides insight into organic acid differences related to expression divergence and domestication in two pear varieties, pinpointing several candidate genes for the genetic manipulation of acidity in pears.

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“…If we focus on “gene targets” governing traits of interest, a well-known example is the domestication of teosinte into the crop maize. It involved “domestication genes” controlling the growth of lateral stems or formation of naked kernels (Chen et al, 2021 ). With genetic and agronomic strategies developed in the last century, additional mutations allowed the cultivation of maize virtually in all places in the world, with remarkably high yields.…”

Section: Basic Lessons From Agriculturementioning

confidence: 99%

“…In schematic terms, improved traits can emerge from specific “rearrangements” or “duplications of chromosomes”. In the simplest example in maize, the crossing of homozygous parent lines can give rise to an heterozygous “hybrid” with superior robustness and productivity, a phenomenon called “heterosis” (Srivastava et al, 2020 ; Chen et al, 2021 ). Polyploidy can also “improve” patterns of gene expression (Schaart et al, 2021 ).…”

Section: Basic Lessons From Agriculturementioning

confidence: 99%

Grand Challenges in Microalgae Domestication

Maréchal

2021

Front. Plant Sci.

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Harnessing Knowledge from Maize and Rice Domestication for New Crop Breeding

Cited by 68 publications

References 196 publications

A high-continuity and annotated tomato reference genome

A high-continuity and annotated tomato reference genome

Transcriptome and Resequencing Analyses Provide Insight into Differences in Organic Acid Accumulation in Two Pear Varieties

Grand Challenges in Microalgae Domestication

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