Linkage and association analyses reveal that hub genes in energy-flow and lipid biosynthesis pathways form a cluster in upland cotton

Gōng, Jǔwǔ; Peng, Yan; Yu, Jie-Ae; Pei, Wenfeng; Zhang, Zhen; Fan, Daoran; Liu, Linjie; Xiao, Xianghui; Liu, Ruixian; Lú, Quánwěi; Li, Pengtao; Shāng, Hǎihóng; Shí, Yùzhēn; Lǐ, Jùnwén; Gě, Qún; Liú, Àiyīng; Dèng, Xiǎoyīng; Fan, Senmiao; Pān, Jìngtāo; Chen, Quanjia; Yuán, Yǒulù; Gǒng, Wànkuí

doi:10.1016/j.csbj.2022.04.012

Cited by 8 publications

(16 citation statements)

References 129 publications

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“…TAG, as the main form of storage oil in seed, is usually detected using high‐performance liquid chromatography‐mass spectrometry combined with electrospray ionization‐mass spectrometry (Komaram et al., 2021). The above‐mentioned high‐throughput determination technologies for the SOC and FAs are currently in use for the identification of transgenic oilseeds in crops (Armenta et al., 2010; Chernova et al., 2021; Gong et al., 2022; Li et al., 2013; Otyama et al., 2022; Pan et al., 2023; Wang et al., 2018).…”

Section: Development Of Determination Technologies For Soc and Fasmentioning

confidence: 99%

Multi‐omics‐driven advances in the understanding of triacylglycerol biosynthesis in oil seeds

Li,

Che,

Zhu

et al. 2023

The Plant Journal

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SUMMARYVegetable oils are rich sources of polyunsaturated fatty acids and energy as well as valuable sources of human food, animal feed, and bioenergy. Triacylglycerols, which are comprised of three fatty acids attached to a glycerol backbone, are the main component of vegetable oils. Here, we review the development and application of multiple‐level omics in major oilseeds and emphasize the progress in the analysis of the biological roles of key genes underlying seed oil content and quality in major oilseeds. Finally, we discuss future research directions in functional genomics research based on current omics and oil metabolic engineering strategies that aim to enhance seed oil content and quality, and specific fatty acids components according to either human health needs or industrial requirements.

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Section: Development Of Determination Technologies For Soc and Fasmentioning

confidence: 99%

Multi‐omics‐driven advances in the understanding of triacylglycerol biosynthesis in oil seeds

Li,

Che,

Zhu

et al. 2023

The Plant Journal

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“…Recently, using the “CCRI70” RILs, “0‐153” RILs, and a natural panel, six interacting genes were identified in the KOC pathway via a linkage analysis of chromatin immunoprecipitation and SLAF‐seq data. Further analysis of differential expression identified four genes ( LtnD , PGK , LPLAT1 , and PAH2 ) which form gene complexes, providing new insights into the mechanisms underlying FA biosynthesis and TAG assembly in cotton seeds (Gong et al, 2022). As illustrated above, many different cotton accessions and populations have been utilized in loci identification using GWAS and QTL mapping.…”

Section: Cotton Functional Genomics: a Magic Weapon For Cotton Breedingmentioning

confidence: 99%

Recent progression and future perspectives in cotton genomic breeding

Yang

Gao

Zhang

et al. 2022

JIPB

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Upland cotton is an important global cash crop for its long seed fibers and high edible oil and protein content. Progress in cotton genomics promotes the advancement of cotton genetics, evolutionary studies, functional genetics, and breeding, and has ushered cotton research and breeding into a new era. Here, we summarize high‐impact genomics studies for cotton from the last 10 years. The diploid Gossypium arboreum and allotetraploid Gossypium hirsutum are the main focus of most genetic and genomic studies. We next review recent progress in cotton molecular biology and genetics, which builds on cotton genome sequencing efforts, population studies, and functional genomics, to provide insights into the mechanisms shaping abiotic and biotic stress tolerance, plant architecture, seed oil content, and fiber development. We also suggest the application of novel technologies and strategies to facilitate genome‐based crop breeding. Explosive growth in the amount of novel genomic data, identified genes, gene modules, and pathways is now enabling researchers to utilize multidisciplinary genomics‐enabled breeding strategies to cultivate “super cotton”, synergistically improving multiple traits. These strategies must rise to meet urgent demands for a sustainable cotton industry.

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“…The cottonseed kernel accumulates 28.24-44.05% vegetable oil [1,3], which provides about 20% of worldwide oil product [2,4] and is recognized as the fifth-largest oil crop in the world, following soybean, palm, canola and sunflower [1]. The fatty acid (FA) composition of cottonseed oil makes it a vital source of vegetable oil, livestock feed and industrial bio-products, including lubricant 2 of 19 oil and biodiesel [3,[5][6][7]. The various unsaturation levels and carbon chain lengths of FAs can be used to define its nutritional and industrial values.…”

Section: Introductionmentioning

confidence: 99%

“…Cottonseed oil is mainly accumulated in kernels of seeds and as the main product of cotton production is lint, the genetic regulatory mechanism of kernel oil content (KOC) accumulation and strategies for its improvement have been paid little attention. Some studies revealed that KOC is regulated in a complex quantitative genetic mechanism and significantly influenced by environmental parameters [7]. Molecular markers are crucial tools for genomic exploration, molecular description, and identification of phenotypic/genetic deviations.…”

Section: Introductionmentioning

confidence: 99%

“…These data have provided useful platforms for genetic marker development via various genotyping by sequencing (GBS) strategies, including specific locus amplified fragment sequencing (SLAFseq), restriction site-associated DNA sequencing (RAD-seq) and microarray sequencing based on molecular hybridization [11]. Several high-density genetic maps (HDGMs) have been constructed using these markers and QTLs of KOC have thus been identified [5,7]. QTL mapping and candidate gene identification have been proven to be the basis of molecular marker-assisted selection (MAS), which has been confirmed to be a robust and operative breeding tool to improve the QTL-controlling traits [11].…”

Section: Introductionmentioning

confidence: 99%

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Hub Genes in Stable QTLs Orchestrate the Accumulation of Cottonseed Oil in Upland Cotton via Catalyzing Key Steps of Lipid-Related Pathways

Alam,

Liu,

Gong

et al. 2023

IJMS

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Upland cotton is the fifth-largest oil crop in the world, with an average supply of nearly 20% of vegetable oil production. Cottonseed oil is also an ideal alternative raw material to be efficiently converted into biodiesel. However, the improvement in kernel oil content (KOC) of cottonseed has not received sufficient attention from researchers for a long time, due to the fact that the main product of cotton planting is fiber. Previous studies have tagged QTLs and identified individual candidate genes that regulate KOC of cottonseed. The regulatory mechanism of oil metabolism and accumulation of cottonseed are still elusive. In the current study, two high-density genetic maps (HDGMs), which were constructed based on a recombinant inbred line (RIL) population consisting of 231 individuals, were used to identify KOC QTLs. A total of forty-three stable QTLs were detected via these two HDGM strategies. Bioinformatic analysis of all the genes harbored in the marker intervals of the stable QTLs revealed that a total of fifty-one genes were involved in the pathways related to lipid biosynthesis. Functional analysis via coexpression network and RNA-seq revealed that the hub genes in the co-expression network that also catalyze the key steps of fatty acid synthesis, lipid metabolism and oil body formation pathways (ACX4, LACS4, KCR1, and SQD1) could jointly orchestrate oil accumulation in cottonseed. This study will strengthen our understanding of oil metabolism and accumulation in cottonseed and contribute to KOC improvement in cottonseed in the future, enhancing the security and stability of worldwide food supply.

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Linkage and association analyses reveal that hub genes in energy-flow and lipid biosynthesis pathways form a cluster in upland cotton

Cited by 8 publications

References 129 publications

Multi‐omics‐driven advances in the understanding of triacylglycerol biosynthesis in oil seeds

Multi‐omics‐driven advances in the understanding of triacylglycerol biosynthesis in oil seeds

Recent progression and future perspectives in cotton genomic breeding

Hub Genes in Stable QTLs Orchestrate the Accumulation of Cottonseed Oil in Upland Cotton via Catalyzing Key Steps of Lipid-Related Pathways

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