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8 pages, 1076 KiB

Open AccessEditorial

Genetic Improvement of Cereals and Grain Legumes

by Muhammad Amjad Nawaz and Gyuhwa Chung

Genes 2020, 11(11), 1255; https://doi.org/10.3390/genes11111255 - 25 Oct 2020

Cited by 11 | Viewed by 3091

Abstract

The anticipated population growth by 2050 will be coupled with increased food demand. To achieve higher and sustainable food supplies in order to feed the global population by 2050, a 2.4% rise in the yield of major crops is required. The key to [...] Read more.

The anticipated population growth by 2050 will be coupled with increased food demand. To achieve higher and sustainable food supplies in order to feed the global population by 2050, a 2.4% rise in the yield of major crops is required. The key to yield improvement is a better understanding of the genetic variation and identification of molecular markers, quantitative trait loci, genes, and pathways related to higher yields and increased tolerance to biotic and abiotic stresses. Advances in genetic technologies are enabling plant breeders and geneticists to breed crop plants with improved agronomic traits. This Special Issue is an effort to report the genetic improvements by adapting genomic techniques and genomic selection. Full article

(This article belongs to the Special Issue Genetic Improvement of Cereals and Grain Legumes)

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Research

Jump to: Editorial

25 pages, 3556 KiB

Open AccessArticle

Multi-Trait Genomic Prediction of Yield-Related Traits in US Soft Wheat under Variable Water Regimes

by Jia Guo, Jahangir Khan, Sumit Pradhan, Dipendra Shahi, Naeem Khan, Muhsin Avci, Jordan Mcbreen, Stephen Harrison, Gina Brown-Guedira, Joseph Paul Murphy, Jerry Johnson, Mohamed Mergoum, Richanrd Esten Mason, Amir M. H. Ibrahim, Russel Sutton, Carl Griffey and Md Ali Babar

Genes 2020, 11(11), 1270; https://doi.org/10.3390/genes11111270 - 28 Oct 2020

Cited by 31 | Viewed by 4651

Abstract

The performance of genomic prediction (GP) on genetically correlated traits can be improved through an interdependence multi-trait model under a multi-environment context. In this study, a panel of 237 soft facultative wheat (Triticum aestivum L.) lines was evaluated to compare single- and [...] Read more.

The performance of genomic prediction (GP) on genetically correlated traits can be improved through an interdependence multi-trait model under a multi-environment context. In this study, a panel of 237 soft facultative wheat (Triticum aestivum L.) lines was evaluated to compare single- and multi-trait models for predicting grain yield (GY), harvest index (HI), spike fertility (SF), and thousand grain weight (TGW). The panel was phenotyped in two locations and two years in Florida under drought and moderately drought stress conditions, while the genotyping was performed using 27,957 genotyping-by-sequencing (GBS) single nucleotide polymorphism (SNP) makers. Five predictive models including Multi-environment Genomic Best Linear Unbiased Predictor (MGBLUP), Bayesian Multi-trait Multi-environment (BMTME), Bayesian Multi-output Regressor Stacking (BMORS), Single-trait Multi-environment Deep Learning (SMDL), and Multi-trait Multi-environment Deep Learning (MMDL) were compared. Across environments, the multi-trait statistical model (BMTME) was superior to the multi-trait DL model for prediction accuracy in most scenarios, but the DL models were comparable to the statistical models for response to selection. The multi-trait model also showed 5 to 22% more genetic gain compared to the single-trait model across environment reflected by the response to selection. Overall, these results suggest that multi-trait genomic prediction can be an efficient strategy for economically important yield component related traits in soft wheat. Full article

(This article belongs to the Special Issue Genetic Improvement of Cereals and Grain Legumes)

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13 pages, 1108 KiB

Open AccessArticle

Improvement of Stable Restorer Lines for Blast Resistance through Functional Marker in Rice (Oryza sativa L.)

by Jegadeesan Ramalingam, Savitha Palanisamy, Ganesh Alagarasan, Vellaichamy Gandhimeyyan Renganathan, Ayyasamy Ramanathan and Ramasamy Saraswathi

Genes 2020, 11(11), 1266; https://doi.org/10.3390/genes11111266 - 27 Oct 2020

Cited by 14 | Viewed by 2750

Abstract

Two popular stable restorer lines, CB 87 R and CB 174 R, were improved for blast resistance through marker-assisted back-cross breeding (MABB). The hybrid rice development program in South India extensively depends on these two restorer lines. However, these restorer lines are highly [...] Read more.

Two popular stable restorer lines, CB 87 R and CB 174 R, were improved for blast resistance through marker-assisted back-cross breeding (MABB). The hybrid rice development program in South India extensively depends on these two restorer lines. However, these restorer lines are highly susceptible to blast disease. To improve the restorer lines for resistance against blasts, we introgressed the broad-spectrum dominant gene Pi54 into these elite restorer lines through two independent crosses. Foreground selection for Pi54 was done by using gene-specific functional marker, Pi54 MAS, at each back-cross generation. Back-crossing was continued until BC₃ and background analysis with seventy polymorphic SSRs covering all the twelve chromosomes to recover the maximum recurrent parent genome was done. At BC₃F₂, closely linked gene-specific/SSR markers, DRRM-RF3-10, DRCG-RF4-8, and RM 6100, were used for the identification of fertility restoration genes, Rf3 and Rf4, along with target gene (Pi54), respectively, in the segregating population. Subsequently, at BC₃F₃, plants, homozygous for the Pi54 and fertility restorer genes (Rf3 and Rf4), were evaluated for blast disease resistance under uniform blast nursery (UBN) and pollen fertility status. Stringent phenotypic selection resulted in the identification of nine near-isogenic lines in CB 87 R × B 95 and thirteen in CB 174 R × B 95 as the promising restorer lines possessing blast disease resistance along with restoration ability. The improved lines also showed significant improvement in agronomic traits compared to the recurrent parents. The improved restorer lines developed through the present study are now being utilized in our hybrid development program. Full article

(This article belongs to the Special Issue Genetic Improvement of Cereals and Grain Legumes)

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26 pages, 3044 KiB

Open AccessArticle

Fine-Mapping of Sorghum Stay-Green QTL on Chromosome10 Revealed Genes Associated with Delayed Senescence

by K. N. S. Usha Kiranmayee, C. Tom Hash, S. Sivasubramani, P. Ramu, Bhanu Prakash Amindala, Abhishek Rathore, P. B. Kavi Kishor, Rajeev Gupta and Santosh P. Deshpande

Genes 2020, 11(9), 1026; https://doi.org/10.3390/genes11091026 - 1 Sep 2020

Cited by 22 | Viewed by 5062

Abstract

This study was conducted to dissect the genetic basis and to explore the candidate genes underlying one of the important genomic regions on an SBI-10 long arm (L), governing the complex stay-green trait contributing to post-flowering drought-tolerance in sorghum. A fine-mapping population was [...] Read more.

This study was conducted to dissect the genetic basis and to explore the candidate genes underlying one of the important genomic regions on an SBI-10 long arm (L), governing the complex stay-green trait contributing to post-flowering drought-tolerance in sorghum. A fine-mapping population was developed from an introgression line cross—RSG04008-6 (stay-green) × J2614-11 (moderately senescent). The fine-mapping population with 1894 F₂ was genotyped with eight SSRs and a set of 152 recombinants was identified, advanced to the F₄ generation, field evaluated with three replications over 2 seasons, and genotyped with the GBS approach. A high-resolution linkage map was developed for SBI-10L using 260 genotyping by sequencing—Single Nucleotide Polymorphism (GBS–SNPs). Using the best linear unpredicted means (BLUPs) of the percent green leaf area (%GL) traits and the GBS-based SNPs, we identified seven quantitative trait loci (QTL) clusters and single gene, mostly involved in drought-tolerance, for each QTL cluster, viz., AP2/ERF transcription factor family (Sobic.010G202700), NBS-LRR protein (Sobic.010G205600), ankyrin-repeat protein (Sobic.010G205800), senescence-associated protein (Sobic.010G270300), WD40 (Sobic.010G205900), CPK1 adapter protein (Sobic.010G264400), LEA2 protein (Sobic.010G259200) and an expressed protein (Sobic.010G201100). The target genomic region was thus delimited from 15 Mb to 8 genes co-localized with QTL clusters, and validated using quantitative real-time (qRT)–PCR. Full article

(This article belongs to the Special Issue Genetic Improvement of Cereals and Grain Legumes)

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18 pages, 2638 KiB

Open AccessArticle

BrEXLB1, a Brassica rapa Expansin-Like B1 Gene Is Associated with Root Development, Drought Stress Response, and Seed Germination

by Muthusamy Muthusamy, Joo Yeol Kim, Eun Kyung Yoon, Jin A. Kim and Soo In Lee

Genes 2020, 11(4), 404; https://doi.org/10.3390/genes11040404 - 8 Apr 2020

Cited by 45 | Viewed by 4490

Abstract

Expansins are structural proteins prevalent in cell walls, participate in cell growth and stress responses by interacting with internal and external signals perceived by the genetic networks of plants. Herein, we investigated the Brassica rapa expansin-like B1 (BrEXLB1) interaction with phytohormones (IAA, ABA, [...] Read more.

Expansins are structural proteins prevalent in cell walls, participate in cell growth and stress responses by interacting with internal and external signals perceived by the genetic networks of plants. Herein, we investigated the Brassica rapa expansin-like B1 (BrEXLB1) interaction with phytohormones (IAA, ABA, Ethephon, CK, GA3, SA, and JA), genes (Bra001852, Bra001958, and Bra003006), biotic (Turnip mosaic Virus (TuMV), Pectobacterium carotovorum, clubroot disease), and abiotic stress (salt, oxidative, osmotic, and drought) conditions by either cDNA microarray or qRT-PCR assays. In addition, we also unraveled the potential role of BrEXLB1 in root growth, drought stress response, and seed germination in transgenic Arabidopsis and B. rapa lines. The qRT-PCR results displayed that BrEXLB1 expression was differentially influenced by hormones, and biotic and abiotic stress conditions; upregulated by IAA, ABA, SA, ethylene, drought, salt, osmotic, and oxidative conditions; and downregulated by clubroot disease, P. carotovorum, and TuMV infections. Among the tissues, prominent expression was observed in roots indicating the possible role in root growth. The root phenotyping followed by confocal imaging of root tips in Arabidopsis lines showed that BrEXLB1 overexpression increases the size of the root elongation zone and induce primary root growth. Conversely, it reduced the seed germination rate. Further analyses with transgenic B. rapa lines overexpressing BrEXLB1 sense (OX) and antisense transcripts (OX-AS) confirmed that BrEXLB1 overexpression is positively associated with drought tolerance and photosynthesis during vegetative growth phases of B. rapa plants. Moreover, the altered expression of BrEXLB1 in transgenic lines differentially influenced the expression of predicted BrEXLB1 interacting genes like Bra001852 and Bra003006. Collectively, this study revealed that BrEXLB1 is associated with root development, drought tolerance, photosynthesis, and seed germination. Full article

(This article belongs to the Special Issue Genetic Improvement of Cereals and Grain Legumes)

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19 pages, 2056 KiB

Open AccessArticle

Comparative Analysis of miRNA Expression Profiles between Heat-Tolerant and Heat-Sensitive Genotypes of Flowering Chinese Cabbage Under Heat Stress Using High-Throughput Sequencing

by Waqas Ahmed, Ronghua Li, Yanshi Xia, Guihua Bai, Kadambot H. M. Siddique, Hua Zhang, Yansong Zheng, Xinquan Yang and Peiguo Guo

Genes 2020, 11(3), 264; https://doi.org/10.3390/genes11030264 - 28 Feb 2020

Cited by 25 | Viewed by 4174

Abstract

Heat stress disturbs cellular homeostasis, thus usually impairs yield of flowering Chinese cabbage (Brassica campestris L. ssp. chinensis var. utilis Tsen et Lee). MicroRNAs (miRNAs) play a significant role in plant responses to different stresses by modulating gene expression at the post-transcriptional [...] Read more.

Heat stress disturbs cellular homeostasis, thus usually impairs yield of flowering Chinese cabbage (Brassica campestris L. ssp. chinensis var. utilis Tsen et Lee). MicroRNAs (miRNAs) play a significant role in plant responses to different stresses by modulating gene expression at the post-transcriptional level. However, the roles that miRNAs and their target genes may play in heat tolerance of flowering Chinese cabbage remain poorly characterized. The current study sequenced six small RNA libraries generated from leaf tissues of flowering Chinese cabbage collected at 0, 6, and 12 h after 38 °C heat treatment, and identified 49 putative novel miRNAs and 43 known miRNAs that differentially expressed between heat-tolerant and heat-sensitive flowering Chinese cabbage. Among them, 14 novel and nine known miRNAs differentially expressed only in the heat-tolerant genotype under heat-stress, therefore, their target genes including disease resistance protein TAO1-like, RPS6, reticuline oxidase-like protein, etc. might play important roles in enhancing heat-tolerance. Gene Ontology (GO) analysis revealed that targets of these differentially expressed miRNAs may play key roles in responses to temperature stimulus, cell part, cellular process, cell, membrane, biological regulation, binding, and catalytic activities. Furthermore, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis identified their important functions in signal transduction, environmental adaptation, global and overview maps, as well as in stress adaptation and in MAPK signaling pathways such as cell death. These findings provide insight into the functions of the miRNAs in heat stress tolerance of flowering Chinese cabbage. Full article

(This article belongs to the Special Issue Genetic Improvement of Cereals and Grain Legumes)

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19 pages, 5489 KiB

Open AccessArticle

Transcriptomic and Metabolomic Changes Triggered by Fusarium solani in Common Bean (Phaseolus vulgaris L.)

by Limin Chen, Quancong Wu, Tianjun He, Jianjun Lan, Li Ding, Tingfu Liu, Qianqian Wu, Yiming Pan and Tingting Chen

Genes 2020, 11(2), 177; https://doi.org/10.3390/genes11020177 - 7 Feb 2020

Cited by 27 | Viewed by 4995

Abstract

Common bean (Phaseolus vulgaris L.) is a major legume and is frequently attacked by fungal pathogens, including Fusarium solani f. sp. phaseoli (FSP), which cause Fusarium root rot. FSP substantially reduces common bean yields across the world, including China, but little is [...] Read more.

Common bean (Phaseolus vulgaris L.) is a major legume and is frequently attacked by fungal pathogens, including Fusarium solani f. sp. phaseoli (FSP), which cause Fusarium root rot. FSP substantially reduces common bean yields across the world, including China, but little is known about how common bean plants defend themselves against this fungal pathogen. In the current study, we combined next-generation RNA sequencing and metabolomics techniques to investigate the changes in gene expression and metabolomic processes in common bean infected with FSP. There were 29,722 differentially regulated genes and 300 differentially regulated metabolites between control and infected plants. The combined omics approach revealed that FSP is perceived by PAMP-triggered immunity and effector-triggered immunity. Infected seedlings showed that common bean responded by cell wall modification, ROS generation, and a synergistic hormone-driven defense response. Further analysis showed that FSP induced energy metabolism, nitrogen mobilization, accumulation of sugars, and arginine and proline metabolism. Importantly, metabolic pathways were most significantly enriched, which resulted in increased levels of metabolites that were involved in the plant defense response. A correspondence between the transcript pattern and metabolite profile was observed in the discussed pathways. The combined omics approach enhances our understanding of the less explored pathosystem and will provide clues for the development of common bean cultivars’ resistant to FSP. Full article

(This article belongs to the Special Issue Genetic Improvement of Cereals and Grain Legumes)

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18 pages, 1933 KiB

Open AccessArticle

Molecular-Assisted Distinctness and Uniformity Testing Using SLAF-Sequencing Approach in Soybean

by Shengrui Zhang, Bin Li, Ying Chen, Abdulwahab S. Shaibu, Hongkun Zheng and Junming Sun

Genes 2020, 11(2), 175; https://doi.org/10.3390/genes11020175 - 6 Feb 2020

Cited by 17 | Viewed by 3545

Abstract

Distinctness, uniformity and stability (DUS) testing of cultivars through morphological descriptors is an important and compulsory part of soybean breeding. Molecular markers are usually more effective and accurate in describing the genetic features for the identification and purity assessment of cultivars. In the [...] Read more.

Distinctness, uniformity and stability (DUS) testing of cultivars through morphological descriptors is an important and compulsory part of soybean breeding. Molecular markers are usually more effective and accurate in describing the genetic features for the identification and purity assessment of cultivars. In the present study, we assessed the distinctness and uniformity of five soybean cultivars using both single nucleotide polymorphism (SNP) markers developed by specific-locus amplified fragment sequencing (SLAF-seq) technology, and simple sequence repeat (SSR) markers. The phylogenetic tree and principal component analysis (PCA) from both the SLAF-seq and SSR methods showed a clear distinction among cultivars Zhonghuang 18, Zhonghuang 68 and Zhonghuang 35, while no clear distinction was observed between cultivars Zhonghuang 13 and Hedou 13. Using the SLAF-seq method, we determined the proportion of homozygous loci for the five soybean cultivars. The heterozygosity of each individual plant was estimated for the assessment of cultivar purity and the purity levels of the five soybean cultivars ranged from 91.89% to 93.96%. To further validate the applicability of the SLAF-seq approach for distinctness testing, we used the SNP information of 150 soybean cultivars with different origins. The cultivars were also distinguished clearly. Taken together, SLAF-seq can be used as an accurate and reliable method in the assessment of the distinctness and uniformity of soybean cultivars. Full article

(This article belongs to the Special Issue Genetic Improvement of Cereals and Grain Legumes)

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16 pages, 2048 KiB

Open AccessArticle

Genomic Selection for Optimum Index with Dry Biomass Yield, Dry Mass Fraction of Fresh Material, and Plant Height in Biomass Sorghum

by Ephrem Habyarimana, Marco Lopez-Cruz and Faheem S. Baloch

Genes 2020, 11(1), 61; https://doi.org/10.3390/genes11010061 - 5 Jan 2020

Cited by 18 | Viewed by 4075

Abstract

Sorghum is one of the world’s major crops, expresses traits for resilience to climate change, and can be used for several purposes including food and clean fuels. Multiple-trait genomic prediction and selection models were implemented using genotyping-by-sequencing single nucleotide polymorphism markers and phenotypic [...] Read more.

Sorghum is one of the world’s major crops, expresses traits for resilience to climate change, and can be used for several purposes including food and clean fuels. Multiple-trait genomic prediction and selection models were implemented using genotyping-by-sequencing single nucleotide polymorphism markers and phenotypic data information. We demonstrated for the first time the efficiency genomic selection modelling of index selection including biofuel traits such as aboveground biomass yield, plant height, and dry mass fraction of the fresh material. This work also sheds light, for the first time, on the promising potential of using the information from the populations grown from seed to predict the performance of the populations regrown from the rhizomes—even two winter seasons after the original trial was sown. Genomic selection modelling of the optimum index selection including the three traits of interest (plant height, aboveground dry biomass yield, and dry mass fraction of fresh mass material) was the most promising. Since the plant characteristics evaluated herein are routinely measured in cereal and other plant species of agricultural interest, it can be inferred that the findings can be transferred in other major crops. Full article

(This article belongs to the Special Issue Genetic Improvement of Cereals and Grain Legumes)

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17 pages, 1525 KiB

Open AccessArticle

Uncovering Phenotypic Diversity and DArTseq Marker Loci Associated with Antioxidant Activity in Common Bean

by Muhammad Azhar Nadeem, Müttalip Gündoğdu, Sezai Ercişli, Tolga Karaköy, Onur Saracoğlu, Ephrem Habyarimana, Xiao Lin, Ruştu Hatipoğlu, Muhammad Amjad Nawaz, Muhammad Sameeullah, Fiaz Ahmad, Bok-Mi Jung, Gyuhwa Chung and Faheem Shehzad Baloch

Genes 2020, 11(1), 36; https://doi.org/10.3390/genes11010036 - 28 Dec 2019

Cited by 27 | Viewed by 5322

Abstract

Antioxidants play an important role in animal and plant life owing to their involvement in complex metabolic and signaling mechanisms, hence uncovering the genetic basis associated with antioxidant activity is very important for the development of improved varieties. Here, a total of 182 [...] Read more.

Antioxidants play an important role in animal and plant life owing to their involvement in complex metabolic and signaling mechanisms, hence uncovering the genetic basis associated with antioxidant activity is very important for the development of improved varieties. Here, a total of 182 common bean (Phaseolus vulgaris) landraces and six commercial cultivars collected from 19 provinces of Turkey were evaluated for seed antioxidant activity under four environments and two locations. Antioxidant activity was measured using ABTS radical scavenging capacity and mean antioxidant activity in common bean landraces was 20.03 µmol TE/g. Analysis of variance reflected that genotype by environment interaction was statistically non-significant and heritability analysis showed higher heritability of antioxidant activity. Variations in seed color were observed, and a higher antioxidant activity was present in seeds having colored seed as compared to those having white seeds. A negative correlation was found between white-colored seeds and antioxidant activity. A total of 7900 DArTseq markers were used to explore the population structure that grouped the studied germplasm into two sub-populations on the basis of their geographical origins and trolox equivalent antioxidant capacity contents. Mean linkage disequilibrium (LD) was 54%, and mean LD decay was 1.15 Mb. Mixed linear model i.e., the Q + K model demonstrated that four DArTseq markers had significant association (p < 0.01) for antioxidant activity. Three of these markers were present on chromosome Pv07, while the fourth marker was located on chromosome Pv03. Among the identified markers, DArT-3369938 marker showed maximum (14.61%) variation. A total of four putative candidate genes were predicted from sequences reflecting homology to identified DArTseq markers. This is a pioneering study involving the identification of association for antioxidant activity in common bean seeds. We envisage that this study will be very helpful for global common bean breeding community in order to develop cultivars with higher antioxidant activity. Full article

(This article belongs to the Special Issue Genetic Improvement of Cereals and Grain Legumes)

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15 pages, 2431 KiB

Open AccessArticle

Effects of Substrate-Binding Site Residues on the Biochemical Properties of a Tau Class Glutathione S-Transferase from Oryza sativa

by Xue Yang, Jinchi Wei, Zhihai Wu and Jie Gao

Genes 2020, 11(1), 25; https://doi.org/10.3390/genes11010025 - 24 Dec 2019

Cited by 8 | Viewed by 4246

Abstract

Glutathione S-transferases (GSTs)—an especially plant-specific tau class of GSTs—are key enzymes involved in biotic and abiotic stress responses. To improve the stress resistance of crops via the genetic modification of GSTs, we predicted the amino acids present in the GSH binding site [...] Read more.

Glutathione S-transferases (GSTs)—an especially plant-specific tau class of GSTs—are key enzymes involved in biotic and abiotic stress responses. To improve the stress resistance of crops via the genetic modification of GSTs, we predicted the amino acids present in the GSH binding site (G-site) and hydrophobic substrate-binding site (H-site) of OsGSTU17, a tau class GST in rice. We then examined the enzyme activity, substrate specificity, enzyme kinetics and thermodynamic stability of the mutant enzymes. Our results showed that the hydrogen bonds between Lys42, Val56, Glu68, and Ser69 of the G-site and glutathione were essential for enzyme activity and thermal stability. The hydrophobic side chains of amino acids of the H-site contributed to enzyme activity toward 4-nitrobenzyl chloride but had an inhibitory effect on enzyme activity toward 1-chloro-2,4-dinitrobenzene and cumene hydroperoxide. Different amino acids of the H-site had different effects on enzyme activity toward a different substrate, 7-chloro-4-nitrobenzo-2-oxa-1,3-diazole. Moreover, Leu112 and Phe162 were found to inhibit the catalytic efficiency of OsGSTU17 to 7-chloro-4-nitrobenzo-2-oxa-1,3-diazole, while Pro16, Leu112, and Trp165 contributed to structural stability. The results of this research enhance the understanding of the relationship between the structure and function of tau class GSTs to improve the abiotic stress resistance of crops. Full article

(This article belongs to the Special Issue Genetic Improvement of Cereals and Grain Legumes)

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17 pages, 4516 KiB

Open AccessArticle

Identification of Key Genes Involved in Embryo Development and Differential Oil Accumulation in Two Contrasting Maize Genotypes

by Xiangxiang Zhang, Meiyan Hong, Heping Wan, Lixia Luo, Zeen Yu and Ruixing Guo

Genes 2019, 10(12), 993; https://doi.org/10.3390/genes10120993 - 1 Dec 2019

Cited by 16 | Viewed by 3228

Abstract

Maize is an important oil seed crop and a major food crop in different parts of the world. Since maize has relatively lower seed oil content as compared to other oil crops, efforts are continuing to improve its oil content percentage. In this [...] Read more.

Maize is an important oil seed crop and a major food crop in different parts of the world. Since maize has relatively lower seed oil content as compared to other oil crops, efforts are continuing to improve its oil content percentage. In this study, we analyzed two contrasting maize genotypes with differential oil accumulation percentages. High oil-content (HOC) maize had 11% oil content while low oil-content (LOC) maize had significantly lower oil content (5.4%). Transmission electron microscopy revealed a higher accumulation of oil bodies in the HOC maize embryo as compared to LOC maize. Comparative RNA-sequencing analysis at different developmental stages of the seed embryos identified 739 genes that are constantly differentially expressed (DEGs) at all the six developmental stages from 15 days after pollination (DAP) to 40 DAP. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis identified fatty acid metabolism and fatty acid biosynthesis as the most enriched biological pathways contributed by these DEGs. Notably, transcriptional changes are more intense at the early stages of embryo development as compared to later stages. In addition, pathways related to oil biosynthesis and their corresponding genes were more enriched at 30 DAP, which seems to be the key stage for oil accumulation. The study also identified 33 key DEGs involved in fatty acid and triacylglycerols biosynthesis, most of which were up-regulated in HOC, that may shape the differential oil contents in the two contrasting maize. Notably, we discovered that both acyl-CoA-dependent and acyl-CoA-independent processes are essential for the high oil accumulation in maize embryo. Full article

(This article belongs to the Special Issue Genetic Improvement of Cereals and Grain Legumes)

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16 pages, 1829 KiB

Open AccessArticle

Genomic Selection for Antioxidant Production in a Panel of Sorghum bicolor and S. bicolor × S. halepense Lines

by Ephrem Habyarimana and Marco Lopez-Cruz

Genes 2019, 10(11), 841; https://doi.org/10.3390/genes10110841 - 24 Oct 2019

Cited by 14 | Viewed by 3272

Abstract

The purpose of this work was to assess the performance of four genomic selection (GS) models (GBLUP, BRR, Bayesian LASSO and BayesB) in 4 sorghum grain antioxidant traits (phenols, flavonoids, total antioxidant capacity and condensed tannins) using whole-genome SNP markers in a novel [...] Read more.

The purpose of this work was to assess the performance of four genomic selection (GS) models (GBLUP, BRR, Bayesian LASSO and BayesB) in 4 sorghum grain antioxidant traits (phenols, flavonoids, total antioxidant capacity and condensed tannins) using whole-genome SNP markers in a novel diversity panel of Sorghum bicolor lines and landraces and S. bicolor × S. halepense recombinant inbred lines. One key breeding problem modelled was predicting the performance in the antioxidant production of new and unphenotyped sorghum genotypes (validation set). The population was weakly structured (analysis of molecular variance, AMOVA R² = 9%), showed a significant genetic diversity and expressed antioxidant traits with a good level of variability and high correlation. The S. bicolor × S. halepense lines outperformed Sorghum bicolor populations for all the antioxidants. The four GS models implemented in this work performed comparably across traits, with accuracy ranging from 0.49 to 0.58, and are considered high enough to sustain sorghum breeding for antioxidants production and allow important genetic gains per unit of time and cost. The results presented in this work are expected to contribute to GS implementation and the genetic improvement of sorghum grain antioxidants for different purposes, including the manufacture of health-promoting and specialty foods. Full article

(This article belongs to the Special Issue Genetic Improvement of Cereals and Grain Legumes)

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