scholarly journals Improving Genomic Prediction for Seed Quality Traits in Oat (Avena sativa L.) Using Trait-Specific Relationship Matrices

2021 ◽  
Vol 12 ◽  
Author(s):  
Malachy T. Campbell ◽  
Haixiao Hu ◽  
Trevor H. Yeats ◽  
Lauren J. Brzozowski ◽  
Melanie Caffe-Treml ◽  
...  

The observable phenotype is the manifestation of information that is passed along different organization levels (transcriptional, translational, and metabolic) of a biological system. The widespread use of various omic technologies (RNA-sequencing, metabolomics, etc.) has provided plant genetics and breeders with a wealth of information on pertinent intermediate molecular processes that may help explain variation in conventional traits such as yield, seed quality, and fitness, among others. A major challenge is effectively using these data to help predict the genetic merit of new, unobserved individuals for conventional agronomic traits. Trait-specific genomic relationship matrices (TGRMs) model the relationships between individuals using genome-wide markers (SNPs) and place greater emphasis on markers that most relevant to the trait compared to conventional genomic relationship matrices. Given that these approaches define relationships based on putative causal loci, it is expected that these approaches should improve predictions for related traits. In this study we evaluated the use of TGRMs to accommodate information on intermediate molecular phenotypes (referred to as endophenotypes) and to predict an agronomic trait, total lipid content, in oat seed. Nine fatty acids were quantified in a panel of 336 oat lines. Marker effects were estimated for each endophenotype, and were used to construct TGRMs. A multikernel TRGM model (MK-TRGM-BLUP) was used to predict total seed lipid content in an independent panel of 210 oat lines. The MK-TRGM-BLUP approach significantly improved predictions for total lipid content when compared to a conventional genomic BLUP (gBLUP) approach. Given that the MK-TGRM-BLUP approach leverages information on the nine fatty acids to predict genetic values for total lipid content in unobserved individuals, we compared the MK-TGRM-BLUP approach to a multi-trait gBLUP (MT-gBLUP) approach that jointly fits phenotypes for fatty acids and total lipid content. The MK-TGRM-BLUP approach significantly outperformed MT-gBLUP. Collectively, these results highlight the utility of using TGRM to accommodate information on endophenotypes and improve genomic prediction for a conventional agronomic trait.

2012 ◽  
Vol 131 (2) ◽  
pp. 434-440 ◽  
Author(s):  
Hajer Trabelsi ◽  
Olfa Aicha Cherif ◽  
Faouzi Sakouhi ◽  
Pierre Villeneuve ◽  
Justin Renaud ◽  
...  

2019 ◽  
Vol 19 (2) ◽  
pp. 285-291
Author(s):  
Dang Thi Phuong Ly ◽  
Nguyen Thi Nga ◽  
Dang Thi Minh Tuyet ◽  
Pham Minh Quan ◽  
Andrey Imbs Borisovich

Five soft coral samples belonging to the same specimen Sinularia brassica were collected in the coastal area of Ha Long Quang Ninh, Nhat Le beach, Quang Binh, Hon Vang - Thanh Hoa and Nha Trang areas (2014–2016), these samples were examined and analyzed by total lipid content, content and composition of lipid and fatty acids. Highest total lipid content was found in the sample SHM 09 collected in Nha Trang bay (1.11%), and the lowest total lipid content was in HL-SHM 07 collected in Ha Long, Quang Ninh (0.68%).The lipid composition of samples contained basic classes such as polar lipids, sterols, free fatty acids, triacylglycerols, monoankyldiacylglycerols, hydrocarbons and waxes. In studied soft corals, there are the appearance of all fatty acids from C12 to C24. There are differences in composition and content of lipids and fatty acids in samples collected in different locations: Samples collected at Nha Trang bay contain more polyunsaturated fatty acids than the other samples collected in Ha Long, Thanh Hoa, Quang Binh. Another two samples, collected in Hon Vang (Thanh Hoa) have similar composition and content of lipid classes, the composition and content of fatty acids in total lipids. The obtained results also show the significant impact of habitat and time of acquisition on the studied subject.


Author(s):  
Onkar Singh Brraich ◽  
Navpreet Kaur ◽  
Swarndeep Singh Hundal

Fish production and fish processing waste have straight connection.  In India, the waste produced during the processing of fish is predicted to be approximate 3.6 million metric tonnes, 48 per cent of the total body weight of Indian and exotic major carps is thrown away as waste (non-edible ). The present research, it was conducted to compare the total lipid content (TLC) and fatty acid composition from the liver of captured and cultured fish, Labeo rohita  (Hamilton) having weight more than 500 gram during different months as well as to evaluate its nutritional quality. Maximum total lipid content (33.33±0.14%) was found in the liver of cultured fish in May month, while the minimum (15.26±0.24%) was in the liver of captured fish in the month of January. During the study, total lipid content was found to be considerably elevated in cultured than captured Fish, Labeo rohita  (Hamilton). The amount of three major groups of fatty acids namely polyunsaturated fatty acids, monounsaturated fatty acids and saturated fatty acids was found to be maximum in captured fish during the month of March 97.19±0.96%, 61.30±0.56% and 95.39±0.31% month of April respectively. Total n-6 polyunsaturated fatty acids were observed to be highest (21.95±8.05%) in the waste of liver in cultured fish during the month of March. Hence, it is concluded that the processing waste (liver) of the captured and cultured, Labeo rohita (Hamilton) is a prosperous resource of the essential fatty acids i.e.  PUFAs and total lipids. Further, it is observed that captured species are rich in fatty acid composition as compared to cultured species. Food industries can manufacture by-products from these high nutritional value contents of   waste for human utilization. EPA and DHA also reduce the risk of various life threatening diseases.


2020 ◽  
Vol 2020 ◽  
pp. 1-9
Author(s):  
Thi Phuong Lan Nguyen ◽  
Van Tuyen Anh Nguyen ◽  
Thi Thanh Trung Do ◽  
Trung Nguyen Quang ◽  
Quoc Long Pham ◽  
...  

The mud crab increases the yield of farming in Southeast Asian countries. Scylla paramamosain, one of four mud crab species belonging to the Scylla genus, is a rich nutrient source during its soft-shell moulting period. In this study, we analysed the total lipid content, fatty acid components, and phospholipid molecular species of the S. paramamosain mud crab. The total lipid content was 1.62 ± 0.08%, which is similar to that of S. serrata previously reported. Twenty-one fatty acids were identified in S. paramamosain. The composition and molecular forms of the phospholipids were identified using high-performance liquid chromatography-high-resolution mass spectrometry. Fifty-four different molecules belonging to six types of phospholipids were identified. Notably, phospholipids were made of fatty acids with C16 : 0; C18 : 0; C20 : 4; C20 : 5; and C22 : 6 main components. The anti-inflammatory and cytotoxic effects of crab lipids and phospholipids were investigated for the first time. The anti-inflammatory activity of the total and polar lipids had IC50 values of 71.5 and 68.6 μg/mL, respectively. The crab polar lipid fraction, which contained phospholipids, also presented high cytotoxic activity toward five cancer cell lines with IC50 values ranging from 85.4 to 95.8 μg/mL.


2020 ◽  
Vol 32 (2) ◽  
pp. 218
Author(s):  
P. Lipinska ◽  
E. Warzych

Studies show that optimal concentrations of fatty acids (FA) and glucose are crucial for proper oocyte development, maturation, and further embryo quality support (Sutton McDowall et al. 2010 Reproduction 139, 685-95, https://doi.org/10.1530/REP-09-0345; Sutton McDowall et al. 2014 Theriogenology 82, 95-103, https://doi.org/10.1016/j.theriogenology.2014.03.011). A balance between metabolism of FA and glucose in oocytes needs to be maintained; however, it is not clear what the preferable pathway of energy production is and how it affects the oocyte. The aim of the experiment was to selectively block pathways of either glucose or FA metabolism during IVM of bovine oocytes to reveal changes within oocyte lipid droplets (LD) under crucial changes in energy metabolism. Cumulus-oocyte complexes were matured under standard conditions (Warzych et al. 2007Mol. Reprod. Dev. 74, 280-289; https://doi.org/10.1002/mrd.20610) without FA and glucose supplementation. The experimental groups were (1) control (IVM in basic medium), (2) group with inhibited glucose metabolism [supplementation with 1.5 µM iodoacetate (IO, inhibitor of glycolysis) and 150 µM dehydroepiandrosterone (DHEA, inhibitor of pentose phosphate pathway)], and (3) group with inhibited FA metabolism (150 µM etomoxir supplementation, ETO). Oocytes after 24h of IVM were stained with boron-dipyrromethene (BODIPY) 493/503 dye (lipid droplets) and 4′,6-diamidino-2-phenylindole (DAPI; chromatin) and analysed using a confocal microscope (LSM 880 AiryScan FAST; Zeiss). Obtained data were analysed using the Kruskal-Wallis test. The MII rate decreased to 60.5% for IO+DHEA (P<0.05) and to 78% for the ETO group compared with the control (83.8%). The average LD area (% of total oocyte area) significantly decreased in both experimental groups (IO+DHEA 6.72±2.5, ETO 6.28±3.2; P<0.01) compared with control (8.7±3.6). Total lipid content (intensity of the fluorescence), was significantly lower in experimental groups (IO+DHEA: 1.17×106±3×105, ETO: 7.1×104±2×104 vs. control: 1.68×106±4.6×105; P<0.01). With regard to the total number of LD, only in the IO+DHEA group were significantly fewer LD noted (987±343; P<0.05), whereas the ETO group did not differ significantly (1146±414) compared with control (1148±357). The ETO group had significantly lower total lipid content (P<0.01) and higher total LD number (P<0.05) compared with IO+DHEA. The area of lipid droplets did not differ between the experimental groups. These results show that blocking glucose metabolism strongly affects the nuclear maturation process of the oocyte, limiting the number of oocytes that reach the MII stage. A significant decrease in total lipid content in the ETO group may suggest strong utilisation of lipids during the maturation process, when de novo synthesis of lipids is blocked. Accumulation of lipids in LD before maturation allows this process to be passed even under the applied FA metabolism inhibitory conditions. In contrast, inhibition of glucose metabolism negatively affects oocyte development strictly after inhibition conditions, indicating the greater significance of glucose for proper oocyte maturation. Further studies are being conducted to investigate the effect of inhibitory systems on lipids in bovine cumulus cells and further embryos. Funding for this study was provided by National Science Centre, Poland (project no 2017/27/B/NZ9/00904).


1979 ◽  
Vol 25 (11) ◽  
pp. 1239-1244 ◽  
Author(s):  
Edward B. Reczek ◽  
David N. Burton

Lipid content and composition were determined in Azotobacter chroococcum grown, under nitrogen-fixing conditions, in continuous culture with intense aeration under atmospheres containing between 5 and 40% O2. Total lipid content remained almost constant at approximately 9% of dry weight.Phospholipid content was maximal at 20% O2 where it accounted for 92% of total lipid, and was minimal at 40% O2. Phosphatidylethanolamine was the only species of phosphatide detected in this fraction. Neutral lipid content was minimal at 20% O2 and maximal at 40% O2 where it represented approximately 30% of the total lipid. Glycolipid remained between 2 and 13% of total lipid throughout. The principal fatty acids of A. chroococcum were hexadecanoic (C16:0), hexadecenoic (C16:1), and octadecenoic acid (C18:1) at all O2 tensions, but C18:1 increased at the expense of C16:1 at higher O2 tensions, particularly in free fatty acid and phospholipid fractions. [U-14C]acetate was readily incorporated into lipid at both 20 and 40% O2 but total incorporation was much greater at 20% O2.


Author(s):  
Zahra Zarei Jeliani ◽  
Nasrin Fazelian ◽  
Morteza Yousefzadi

Abstract The aim of this work was to describe and compare the main fatty acids and biodiesel indices of some green and brown macroalgae (seaweeds) collected from the Persian Gulf, as an alternative raw material for renewable biodiesel production. The macroalgae showed low lipid content (< 10% DW) but marine macroalgae with total lipid content > 5% DW are a good source for biodiesel production. The total lipid content and saturated fatty acids (SFAs) of green algae were higher than that of brown algae, while higher accumulation of unsaturated fatty acids (USFAs) was observed in brown seaweeds. Further, the main fatty acid in all studied seaweeds was palmitic acid (C16:0), which was followed by oleic acid (C18:1). The results of this work showed that three of the green algae, especially C. sertularioides, could be a potential source of fatty acids for biodiesel production owing to their high total lipid content, high cold flow indices (long chain saturated factor, cold filter plugging point and cloud point) and a fatty acid profile rich in SFAs with a high amount of C18:1, which is suitable for oil-based bio products. In contrast, the brown seaweeds Sargassum boveanum and Sirophysalis trinodis lipid content had a high proportion of polyunsaturated fatty acids (PUFAs), which makes them suitable for replacing fish oil.


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