Combined Transcriptome and Lipidomic Analyses of Lipid Biosynthesis in Macadamia ternifolia Nuts

Macadamia nuts are considered a high-quality oil crop worldwide. To date, the lipid diversity and the genetic factors that mediate storage lipid biosynthesis in Macadamia ternifolia are poorly known. Here, we performed a comprehensive transcriptomic and lipidomic data analysis to understand the mechanism of lipid biosynthesis by using young, medium-aged, and mature fruit kernels. Our lipidomic analysis showed that the M. ternifolia kernel was a rich source of unsaturated fatty acids. Moreover, different species of triacylglycerols, diacylglycerol, ceramides, phosphatidylethanolamine, and phosphatidic acid had altered accumulations during the developmental stages. The transcriptome analysis revealed a large percentage of differently expressed genes during the different stages of macadamia growth. Most of the genes with significant differential expression performed functional activity of oxidoreductase and were enriched in the secondary metabolite pathway. The integration of lipidomic and transcriptomic data allowed for the identification of glycerol-3-phosphate acyltransferase, diacylglycerol kinase, phosphatidylinositols, nonspecific phospholipase C, pyruvate kinase 2, 3-ketoacyl-acyl carrier protein reductase, and linoleate 9S-lipoxygenase as putative candidate genes involved in lipid biosynthesis, storage, and oil quality. Our study found comprehensive datasets of lipidomic and transcriptomic changes in the developing kernel of M. ternifolia. In addition, the identification of candidate genes provides essential prerequisites to understand the molecular mechanism of lipid biosynthesis in the kernel of M. ternifolia.

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Molecular Marker Mapping of Genes Enhancing Tocol and Carotenoid Composition of Maize Grain

10.32747/1995.7571352.bard ◽

1995 ◽

Author(s):

Torbert Rocheford ◽

Yaakov Tadmor ◽

Robert Lambert ◽

Nurit Katzir

Keyword(s):

Molecular Marker ◽

Vitamin A ◽

Candidate Genes ◽

Ssr Markers ◽

Unsaturated Fatty Acids ◽

Oil Quality ◽

Total Carotenoids ◽

Animal Feeding ◽

Maize Grain ◽

The Cost

The overall objective of this research was to identify chromosomal regions and candidate genes associated with control of concentration and forms of carotenoids (includes pro-Vitamin A) and tocopherols (Vitamin E), which are both antioxidants and are associated with health advantages. Vitamin A and E are included in animal feeding supplements and the eventual goal is to increase levels of these compounds in maize grain so that the cost of these supplements can be reduced or eliminated. Moreover, both compounds are antioxidants that protect unsaturated fatty acids from oxidation and thus maintaining maize oil quality for longer periods. We identified three SSR markers that are associated with 38% of the variation for total carotenoids and three SSR markers associated with 44% of the variation for total tocopherols in the cross W64a x A632. We identified two candidate genes associated with levels of carotenoids: phytoene synthase and zeta carotene desaturase. Evaluation of (Illinois High Oil x B73) B73 BC 1S1 population for tocopherols detected additional chromosomal regions influencing the level of total tocopherols, and detected a common region on chromosome 5 associated with ratio of the more desirable alpha from to the gamma form of tocopherol. The results suggest molecular marker assisted selection for higher levels of these antioxidants in corn grain should be feasible.

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Insights into triterpene synthesis and unsaturated fatty-acid accumulation provided by chromosomal-level genome analysis of Akebia trifoliata subsp. australis

Horticulture Research ◽

10.1038/s41438-020-00458-y ◽

2021 ◽

Vol 8 (1) ◽

Author(s):

Hui Huang ◽

Juan Liang ◽

Qi Tan ◽

Linfeng Ou ◽

Xiaolin Li ◽

...

Keyword(s):

Fatty Acids ◽

Fatty Acid ◽

Unsaturated Fatty Acids ◽

Developmental Stages ◽

De Novo ◽

Acyl Carrier Protein ◽

Repetitive Sequences ◽

Gene Families ◽

Terpene Synthase ◽

Comparative Genomic

AbstractAkebia trifoliata subsp. australis is a well-known medicinal and potential woody oil plant in China. The limited genetic information available for A. trifoliata subsp. australis has hindered its exploitation. Here, a high-quality chromosome-level genome sequence of A. trifoliata subsp. australis is reported. The de novo genome assembly of 682.14 Mb was generated with a scaffold N50 of 43.11 Mb. The genome includes 25,598 protein-coding genes, and 71.18% (485.55 Mb) of the assembled sequences were identified as repetitive sequences. An ongoing massive burst of long terminal repeat (LTR) insertions, which occurred ~1.0 million years ago, has contributed a large proportion of LTRs in the genome of A. trifoliata subsp. australis. Phylogenetic analysis shows that A. trifoliata subsp. australis is closely related to Aquilegia coerulea and forms a clade with Papaver somniferum and Nelumbo nucifera, which supports the well-established hypothesis of a close relationship between basal eudicot species. The expansion of UDP-glucoronosyl and UDP-glucosyl transferase gene families and β-amyrin synthase-like genes and the exclusive contraction of terpene synthase gene families may be responsible for the abundant oleanane-type triterpenoids in A. trifoliata subsp. australis. Furthermore, the acyl-ACP desaturase gene family, including 12 stearoyl-acyl-carrier protein desaturase (SAD) genes, has expanded exclusively. A combined transcriptome and fatty-acid analysis of seeds at five developmental stages revealed that homologs of SADs, acyl-lipid desaturase omega fatty acid desaturases (FADs), and oleosins were highly expressed, consistent with the rapid increase in the content of fatty acids, especially unsaturated fatty acids. The genomic sequences of A. trifoliata subsp. australis will be a valuable resource for comparative genomic analyses and molecular breeding.

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Comprehensive analysis and identification of drought-responsive candidate NAC genes in three semi-arid tropics (SAT) legume crops

BMC Genomics ◽

10.1186/s12864-021-07602-5 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Sadhana Singh ◽

Himabindu Kudapa ◽

Vanika Garg ◽

Rajeev K. Varshney

Keyword(s):

Drought Stress ◽

Candidate Genes ◽

Developmental Stages ◽

Biological Activities ◽

Expression Patterns ◽

Genome Wide ◽

Legume Crops ◽

Root Tissues ◽

Semi Arid ◽

Comprehensive Study

Abstract Background Chickpea, pigeonpea, and groundnut are the primary legume crops of semi-arid tropics (SAT) and their global productivity is severely affected by drought stress. The plant-specific NAC (NAM - no apical meristem, ATAF - Arabidopsis transcription activation factor, and CUC - cup-shaped cotyledon) transcription factor family is known to be involved in majority of abiotic stresses, especially in the drought stress tolerance mechanism. Despite the knowledge available regarding NAC function, not much information is available on NAC genes in SAT legume crops. Results In this study, genome-wide NAC proteins – 72, 96, and 166 have been identified from the genomes of chickpea, pigeonpea, and groundnut, respectively, and later grouped into 10 clusters in chickpea and pigeonpea, while 12 clusters in groundnut. Phylogeny with well-known stress-responsive NACs in Arabidopsis thaliana, Oryza sativa (rice), Medicago truncatula, and Glycine max (soybean) enabled prediction of putative stress-responsive NACs in chickpea (22), pigeonpea (31), and groundnut (33). Transcriptome data revealed putative stress-responsive NACs at various developmental stages that showed differential expression patterns in the different tissues studied. Quantitative real-time PCR (qRT-PCR) was performed to validate the expression patterns of selected stress-responsive, Ca_NAC (Cicer arietinum - 14), Cc_NAC (Cajanus cajan - 15), and Ah_NAC (Arachis hypogaea - 14) genes using drought-stressed and well-watered root tissues from two contrasting drought-responsive genotypes of each of the three legumes. Based on expression analysis, Ca_06899, Ca_18090, Ca_22941, Ca_04337, Ca_04069, Ca_04233, Ca_12660, Ca_16379, Ca_16946, and Ca_21186; Cc_26125, Cc_43030, Cc_43785, Cc_43786, Cc_22429, and Cc_22430; Ah_ann1.G1V3KR.2, Ah_ann1.MI72XM.2, Ah_ann1.V0X4SV.1, Ah_ann1.FU1JML.2, and Ah_ann1.8AKD3R.1 were identified as potential drought stress-responsive candidate genes. Conclusion As NAC genes are known to play role in several physiological and biological activities, a more comprehensive study on genome-wide identification and expression analyses of the NAC proteins have been carried out in chickpea, pigeonpea and groundnut. We have identified a total of 21 potential drought-responsive NAC genes in these legumes. These genes displayed correlation between gene expression, transcriptional regulation, and better tolerance against drought. The identified candidate genes, after validation, may serve as a useful resource for molecular breeding for drought tolerance in the SAT legume crops.

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Evaluation of some sunflower genotypes for agronomic traits and oil quality

Helia ◽

10.1515/helia-2020-0027 ◽

2021 ◽

Vol 0 (0) ◽

Author(s):

Khaled Mohamed Aboelkassem ◽

Asmaa Abd-EL-Halime Ahmed ◽

Mohamed Ali Abdelsatar

Keyword(s):

Fatty Acids ◽

Seed Yield ◽

Seed Weight ◽

Unsaturated Fatty Acids ◽

Agronomic Traits ◽

Oil Quality ◽

Research Station ◽

Head Diameter ◽

Coefficients Of Variation ◽

100 Seed Weight

Abstract The present investigation was carried out to evaluate agronomic performance and oil quality of seven sunflower genotypes at Shandaweel Research Station, Agricultural Research Center, Sohag, Egypt during 2018 and 2019 summer seasons. These genetic materials were sown in a randomized complete block design having three replications. Significant genetic variations among evaluated sunflower genotypes for agronomic traits and oil quality were observed. The superior sunflower genotypes were Line 120 for seed yield per hectare (3102.38 kg), Sakha 53 for seed oil content (44.63 %) and Line 125 for oil quality where it contained the highest proportion of unsaturated fatty acids (89.20 %). The phenotypic coefficients of variation were slightly higher than genotypic coefficients of variation for all studied traits. High heritability (exceeded 60%) and genetic advance as percent of mean (ranged from medium to high, exceeded 10%) was observed for most studied traits. Seed yield per plant positively correlated with plant height, stem diameter, head diameter, and 100-seed weight and most chemical traits at phenotypic and genotypic levels. Maximum phenotypic direct effects on seed yield per plant were observed for 100-seed weight, head diameter and total unsaturated fatty acids. While, the highest genotypic direct effect on seed yield per plant was observed for head diameter. Hence, most studied traits could be employed as selection criteria for improving evaluated sunflower genotypes.

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The Effect of Salinity and Irrigation Regimes on the Level of Fatty Acids in Olive Flesh Oil

Modern Applied Science ◽

10.5539/mas.v10n5p98 ◽

2016 ◽

Vol 10 (5) ◽

pp. 98

Author(s):

Ali Asghar Ghaemi ◽

Ali Dindarlou ◽

Mohammad Taghi Golmakani ◽

Fatemeh Razzaghi

Keyword(s):

Fatty Acids ◽

Palmitic Acid ◽

Irrigation Water ◽

Field Experiments ◽

Unsaturated Fatty Acids ◽

Saline Water ◽

Oil Quality ◽

Irrigation Treatment ◽

Water Levels ◽

Irrigation Levels

Olive trees have the capability of growing under semi-arid regions, where drought and salinity are the major concerns. Two years field experiments were carried out to investigate the interaction effects of natural saline well water and irrigation levels on the quantity and quality of fatty acids in the olive flesh fruits (“Roghani” cultivar). A factorial layout within a randomized complete blocks design with three replications of five irrigation levels (I1 to I5 as 0.25, 0.5, 0.75, 1 and 1.25 ETc) and three saline water levels (S1 to S3 as 100%WW, 50%WW+50%FW and 100%FW) were considered. The fresh and brackish irrigation water were withdrawn from two different natural wells (fresh water (FW) and saline water wells (WW)). Results revealed that increasing salinity and decreasing irrigation water levels caused significant increment in the ratio of unsaturated fatty acids, palmitic acid to the percentage of oil and oil percentage in olive flesh fruit. It is found that as water salinity increased from lowest to the highest level, the oleic acid trends to its highest value of 23.68% in I1S1. Mean values of palmitic acid in 2013 were 27.52% and decreased to 19% in 2014. It is concluded that highest percentage of oleic, linoleic, linolenic and palmitic acids obtained under high saline and less applied irrigation treatment (S1I2) yielding to improve the olive oil quality.

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FabF Is Required for Piezoregulation ofcis-Vaccenic Acid Levels and Piezophilic Growth of the Deep-Sea Bacterium Photobacterium profundum Strain SS9

Journal of Bacteriology ◽

10.1128/jb.182.5.1264-1271.2000 ◽

2000 ◽

Vol 182 (5) ◽

pp. 1264-1271 ◽

Cited By ~ 41

Author(s):

Eric E. Allen ◽

Douglas H. Bartlett

Keyword(s):

High Pressure ◽

Hydrostatic Pressure ◽

Deep Sea ◽

Unsaturated Fatty Acids ◽

Acyl Carrier Protein ◽

Vaccenic Acid ◽

Bacterial Species ◽

Elevated Pressure ◽

Wild Type ◽

Photobacterium Profundum

ABSTRACT To more fully explore the role of unsaturated fatty acids in high-pressure, low-temperature growth, the fabF gene from the psychrotolerant, piezophilic deep-sea bacteriumPhotobacterium profundum strain SS9 was characterized and its role and regulation were examined. An SS9 strain harboring a disruption in the fabF gene (strain EA40) displayed growth impairment at elevated hydrostatic pressure concomitant with diminishedcis-vaccenic acid (18:1) production. However, growth ability at elevated pressure could be restored to wild-type levels by the addition of exogenous 18:1 to the growth medium. Transcript analysis did not indicate that the SS9 fabF gene is transcriptionally regulated, suggesting that the elevated 18:1 levels produced in response to pressure increase result from posttranscriptional changes. Unlike many pressure-adapted bacterial species such as SS9, the mesophile Escherichia coli did not regulate its fatty acid composition in an adaptive manner in response to changes in hydrostatic pressure. Moreover, an E. coli fabF strain was as susceptible to elevated pressure as wild-type cells. It is proposed that the SS9 fabF product, β-ketoacyl–acyl carrier protein synthase II has evolved novel pressure-responsive characteristics which facilitate SS9 growth at high pressure.

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Genome-wide comparative analysis of the BAHD superfamily in seven Rosaceae species and expression analysis in pear (Pyrus☓ bretschneideri)

10.21203/rs.2.13258/v3 ◽

2019 ◽

Author(s):

Chunxin Liu ◽

Xin Qiao ◽

Qionghou Li ◽

Weiwei Zeng ◽

Shuwei Wei ◽

...

Keyword(s):

Comparative Analysis ◽

Candidate Genes ◽

Fruit Quality ◽

Prunus Persica ◽

Prunus Avium ◽

Developmental Stages ◽

Purifying Selection ◽

Pear Fruit ◽

Rosaceae Species ◽

Expression Characteristics

Abstract Background: The BAHD acyltransferase superfamily exhibits various biological roles in plants, including regulating fruit quality, catalytic synthesizing of terpene, phenolics and esters, and improving stress resistance. However, the copy numbers, expression characteristics and associations with fruit aroma formation of the BAHD genes remain unclear. Results: In total, 717 BAHD genes were obtained from the genomes of seven Rosaceae , ( Pyrus bretschneideri , Malus domestica , Prunus avium , Prunus persica , Fragaria vesca , Pyrus communis and Rubus occidentalis ). Based on the detailed phylogenetic analysis and classifications in model plants, we divided the BAHD family genes into seven groups, I-a, I-b, II-a, II-b, III-a, IV and V. An inter-species synteny analysis revealed the ancient origin of BAHD superfamily with 78 syntenic gene pairs were detected among the seven Rosaceae species. Different types of gene duplication events jointly drive the expansion of BAHD superfamily, and purifying selection dominates the evolution of BAHD genes supported by the small Ka/Ks ratios . Based on the correlation analysis between the ester content and expression levels of BAHD genes at different developmental stages, four candidate genes were selected for verification as assessed by qRT-PCR. The result implied that Pbr020016.1 , Pbr019034.1 , Pbr014028.1 and Pbr029551.1 are important candidate genes involved in aroma formation during pear fruit development. Conclusion: We have thoroughly identified the BAHD superfamily genes and performed a comprehensive comparative analysis of their phylogenetic relationships, expansion patterns, and expression characteristics in seven Rosaceae species, and we also obtained four candidate genes involved in aroma synthesis in pear fruit . These results provide a theoretical basis for future studies of the specific biological functions of BAHD superfamily members and the improvement of pear fruit quality. Keywords : BAHD, pear, evolution, Rosaceae, transcriptome, volatile esters

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Comprehensive Transcriptome Analyses Reveal Candidate Genes for Variation in Seed Size/Weight During Peanut (Arachis hypogaea L.) Domestication

Frontiers in Plant Science ◽

10.3389/fpls.2021.666483 ◽

2021 ◽

Vol 12 ◽

Author(s):

Zhongfeng Li ◽

Xingguo Zhang ◽

Kunkun Zhao ◽

Kai Zhao ◽

Chengxin Qu ◽

...

Keyword(s):

Candidate Genes ◽

Seed Development ◽

Seed Size ◽

Snp Markers ◽

Pentatricopeptide Repeat ◽

Significant Differential Expression ◽

Ppr Protein ◽

Cultivated Peanut ◽

Transcriptome Analyses ◽

Wild Peanut

Seed size/weight, a key domestication trait, is also an important selection target during peanut breeding. However, the mechanisms that regulate peanut seed development are unknown. We re-sequenced 12 RNA samples from developing seeds of two cultivated peanut accessions (Lines 8106 and 8107) and wild Arachis monticola at 15, 30, 45, and 60 days past flowering (DPF). Transcriptome analyses showed that ∼36,000 gene loci were expressed in each of the 12 RNA samples, with nearly half exhibiting moderate (2 ≤ FPKM < 10) expression levels. Of these genes, 12.2% (4,523) were specifically expressed during seed development, mainly at 15 DPF. Also, ∼12,000 genes showed significant differential expression at 30, 45, and/or 60 DPF within each of the three peanut accessions, accounting for 31.8–34.1% of the total expressed genes. Using a method that combined comprehensive transcriptome analysis and previously mapped QTLs, we identified several candidate genes that encode transcription factor TGA7, topless-related protein 2, IAA-amino acid hydrolase ILR1-like 5, and putative pentatricopeptide repeat-containing (PPR) protein. Based on sequence variations identified in these genes, SNP markers were developed and used to genotype both 30 peanut landraces and a genetic segregated population, implying that EVM0025654 encoding a PPR protein may be associated with the increased seed size/weight of the cultivated accessions in comparison with the allotetraploid wild peanut. Our results provide additional knowledge for the identification and functional research into candidate genes responsible for the seed size/weight phenotype in peanut.

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Identification of genetic factors controlling phosphorus utilization efficiency in wheat by genome-wide association study with principal component analysis

10.1101/2020.09.04.283556 ◽

2020 ◽

Author(s):

Luqman Bin Safdar ◽

Muhammad Jawad Umer ◽

Fakhrah Almas ◽

Siraj Uddin ◽

Qurra-tul-Ain Safdar ◽

...

Keyword(s):

Association Study ◽

Candidate Genes ◽

Genetic Factors ◽

Genome Wide Association Study ◽

Principal Component ◽

Utilization Efficiency ◽

Genome Wide Association ◽

Genome Wide ◽

P Utilization ◽

P Utilization Efficiency

ABSTRACTDespite the economic importance of P utilization efficiency, information on genetic factors underlying this trait remains elusive. To address that, we performed a genome-wide association study in a spring wheat diversity panel ranging from landraces to elite varieties. We evaluated the phenotype variation for P utilization efficiency in controlled conditions and genotype variation using wheat 90K SNP array. Phenotype variables were transformed into a smaller set of uncorrelated principal components that captured the most important variation data. We identified two significant loci associated with both P utilization efficiency and the 1st principal component on chromosomes 3A and 4A: qPE1-3A and qPE2-4A. Annotation of genes at these loci revealed 53 wheat genes, among which 6 were identified in significantly enriched pathways. The expression pattern of these 6 genes indicated that TraesCS4A02G481800, involved in pyruvate metabolism and TCA cycle, had a significantly higher expression in the P efficient variety under limited P conditions. Further characterization of these loci and candidate genes can help stimulate P utilization efficiency in wheat.KEY MESSAGEWe report two new loci for P utilization efficiency on chromosomes 3A and 4A of wheat. The prioritized candidate genes at these loci can be investigated by molecular biology techniques to improve P efficiency in wheat and grass relatives.

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Genome-Wide Association Studies of 39 Seed Yield-Related Traits in Sesame (Sesamum indicum L.)

International Journal of Molecular Sciences ◽

10.3390/ijms19092794 ◽

2018 ◽

Vol 19 (9) ◽

pp. 2794 ◽

Cited By ~ 5

Author(s):

Rong Zhou ◽

Komivi Dossa ◽

Donghua Li ◽

Jingyin Yu ◽

Jun You ◽

...

Keyword(s):

Candidate Genes ◽

Seed Yield ◽

Association Studies ◽

Oil Quality ◽

Genome Wide Association ◽

Oilseed Crop ◽

Genome Wide Association Studies ◽

Genome Wide ◽

Highly Correlated ◽

Capsule Size

Sesame is poised to become a major oilseed crop owing to its high oil quality and adaptation to various ecological areas. However, the seed yield of sesame is very low and the underlying genetic basis is still elusive. Here, we performed genome-wide association studies of 39 seed yield-related traits categorized into five major trait groups, in three different environments, using 705 diverse lines. Extensive variation was observed for the traits with capsule size, capsule number and seed size-related traits, found to be highly correlated with seed yield indexes. In total, 646 loci were significantly associated with the 39 traits (p < 10−7) and resolved to 547 quantitative trait loci QTLs. We identified six multi-environment QTLs and 76 pleiotropic QTLs associated with two to five different traits. By analyzing the candidate genes for the assayed traits, we retrieved 48 potential genes containing significant functional loci. Several homologs of these candidate genes in Arabidopsis are described to be involved in seed or biomass formation. However, we also identified novel candidate genes, such as SiLPT3 and SiACS8, which may control capsule length and capsule number traits. Altogether, we provided the highly-anticipated basis for research on genetics and functional genomics towards seed yield improvement in sesame.

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