scholarly journals Simultaneous Dissection of Grain Carotenoid Levels and Kernel Color in Biparental Maize Populations with Yellow-to-Orange Grain

2021 ◽  
Author(s):  
Mary-Francis LaPorte ◽  
Mishi Vachev ◽  
Matthew Fenn ◽  
Christine Diepenbrock
Keyword(s):  
Genome Wide Association Study ◽  
Vitamin A Deficiency ◽  
Provitamin A ◽  
Human Populations ◽  
Carotenoid Cleavage Dioxygenase ◽  
Total Carotenoids ◽  
Nested Association Mapping ◽  
Kernel Color ◽  
A Genome ◽  
Variation Explained

ABSTRACTMaize enriched in provitamin A carotenoids could be key in combatting vitamin A deficiency in human populations relying on maize as a food staple. Consumer studies indicate that orange maize may be regarded as novel and preferred. This study identifies genes of relevance for grain carotenoid concentrations and kernel color, through simultaneous dissection of these traits in 10 families of the U.S. maize nested association mapping population that have yellow to orange grain. Quantitative trait loci (QTL) were identified via joint-linkage analysis, with phenotypic variation explained for individual kernel color QTL ranging from 2.4 to 17.5%. These QTL were cross-analyzed with significant marker-trait associations in a genome-wide association study that utilized ∼27 million variants. Nine genes were identified: four encoding activities upstream of the core carotenoid pathway, one at the pathway branchpoint, three within the α- or β-pathway branches, and one encoding a carotenoid cleavage dioxygenase. Of these, three exhibited significant pleiotropy between kernel color and one or more carotenoid traits. Kernel color exhibited moderate positive correlations with β-branch and total carotenoids and negligible correlations with α-branch carotenoids. These findings can be leveraged to simultaneously achieve desirable kernel color phenotypes and increase concentrations of provitamin A and other priority carotenoids.

scholarly journals Simultaneous Dissection of Grain Carotenoid Levels and Kernel Color in Biparental Maize Populations with Yellow-to-Orange Grain

2022 ◽  
Author(s):  
Mary-Francis LaPorte ◽  
Mishi Vachev ◽  
Matthew Fenn ◽  
Christine Diepenbrock
Keyword(s):  
Genome Wide Association Study ◽  
Vitamin A Deficiency ◽  
Provitamin A ◽  
Human Populations ◽  
Carotenoid Cleavage Dioxygenase ◽  
Total Carotenoids ◽  
Nested Association Mapping ◽  
Kernel Color ◽  
Mapping Panel ◽  
A Genome

ABSTRACT Maize enriched in provitamin A carotenoids could be key in combatting vitamin A deficiency in human populations relying on maize as a food staple. Consumer studies indicate that orange maize may be regarded as novel and preferred. This study identifies genes of relevance for grain carotenoid concentrations and kernel color, through simultaneous dissection of these traits in 10 families of the U.S. maize nested association mapping panel that have yellow to orange grain. Quantitative trait loci (QTL) were identified via joint-linkage analysis, with phenotypic variation explained for individual kernel color QTL ranging from 2.4 to 17.5%. These QTL were cross-analyzed with significant marker-trait associations in a genome-wide association study that utilized ∼27 million variants. Nine genes were identified: four encoding activities upstream of the core carotenoid pathway, one at the pathway branchpoint, three within the α- or β-pathway branches, and one encoding a carotenoid cleavage dioxygenase. Of these, three exhibited significant pleiotropy between kernel color and one or more carotenoid traits. Kernel color exhibited moderate positive correlations with β-branch and total carotenoids and negligible correlations with α-branch carotenoids. These findings can be leveraged to simultaneously achieve desirable kernel color phenotypes and increase concentrations of provitamin A and other priority carotenoids.

scholarly journals Genome-Wide Association Study and Pathway-Level Analysis of Kernel Color in Maize

2019 ◽  
Author(s):  
Brenda F. Owens ◽  
Deepu Mathew ◽  
Christine H. Diepenbrock ◽  
Tyler Tiede ◽  
Di Wu ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Carotenoid Biosynthesis ◽  
Provitamin A ◽  
Genome Wide Association ◽  
Kernel Color ◽  
Genome Wide ◽  
A Genome ◽  
Level Analysis ◽  
Pathway Level

ABSTRACTRapid development and adoption of biofortified, provitamin A-dense orange maize (Zea mays L.) varieties could be facilitated by a greater understanding of the natural variation underlying kernel color, including as relates to carotenoid biosynthesis and retention in maize grain. Greater abundance of carotenoids in maize kernels is generally accompanied by deeper orange color, useful for distinguishing provitamin A-dense varieties to consumers. While kernel color can be scored and selected with high-throughput, low-cost phenotypic methods within breeding selection programs, it remains to be well established as to what would be the logical genetic loci to target for selection for kernel color. We conducted a genome-wide association study of maize kernel color, as determined by colorimetry, in 1,651 yellow and orange inbreds from the Ames maize inbred panel. Associations were found with y1, encoding the first committed step in carotenoid biosynthesis, and with dxs2, which encodes the enzyme responsible for the first committed step in the biosynthesis of the isoprenoid precursors of carotenoids. These genes logically could contribute to overall carotenoid abundance and thus kernel color. The lcyE and zep1 genes, which can affect carotenoid composition, were also found to be associated with colorimeter values. A pathway-level analysis, focused on genes with a priori evidence of involvement in carotenoid biosynthesis and retention, revealed associations for dxs3 and dmes1, involved in isoprenoid biosynthesis; ps1 and vp5, within the core carotenoid pathway; and vp14, involved in cleavage of carotenoids. Collectively, these identified genes appear relevant to the accumulation of kernel color.

scholarly journals Development of sub-tropically adapted diverse provitamin-A rich maize inbreds through marker-assisted pedigree selection, their characterization and utilization in hybrid breeding

PLoS ONE ◽  
2021 ◽  
Vol 16 (2) ◽  
pp. e0245497
Author(s):  
Hriipulou Duo ◽  
Firoz Hossain ◽  
Vignesh Muthusamy ◽  
Rajkumar U. Zunjare ◽  
Rajat Goswami ◽  
...  
Keyword(s):  
Grain Yield ◽  
Gene Diversity ◽  
Vitamin A Deficiency ◽  
Genetic Relationships ◽  
Cost Effective ◽  
Provitamin A ◽  
Hybrid Breeding ◽  
Environment Interaction ◽  
Total Carotenoids ◽  
Pedigree Breeding

Malnutrition has emerged as one of the major health problems worldwide. Traditional yellow maize has low provitamin-A (proA) content and its genetic base in proA biofortification breeding program of subtropics is extremely narrow. To diversify the proA rich germplasm, 10 elite low proA inbreds were crossed with a proA rich donor (HP702-22) having mutant crtRB1 gene. The F2 populations derived from these crosses were genotyped using InDel marker specific to crtRB1. Severe marker segregation distortion was observed. Seventeen crtRB1 inbreds developed through marker-assisted pedigree breeding and seven inbreds generated using marker-assisted backcross breeding were characterized using 77 SSRs. Wide variation in gene diversity (0.08 to 0.79) and dissimilarity coefficient (0.28 to 0.84) was observed. The inbreds were grouped into three major clusters depicting the existing genetic diversity. The crtRB1-based inbreds possessed high β-carotene (BC: 8.72μg/g), β-cryptoxanthin (BCX: 4.58μg/g) and proA (11.01μg/g), while it was 2.35μg/g, 1.24μg/g and 2.97μg/g in checks, respectively. Based on their genetic relationships, 15 newly developed crtRB1-based inbreds were crossed with five testers (having crtRB1 gene) using line × tester mating design. 75 experimental hybrids with crtRB1 gene were evaluated over three locations. These experimental hybrids possessed higher BC (8.02μg/g), BCX (4.69μg/g), proA (10.37μg/g) compared to traditional hybrids used as check (BC: 2.36 μg/g, BCX: 1.53μg/g, proA: 3.13μg/g). Environment and genotypes × environment interaction had minor effects on proA content. Both additive and dominance gene action were significant for proA. The mean proportion of proA to total carotenoids (TC) was 44% among crtRB1-based hybrids, while 11% in traditional hybrids. BC was found to be positively correlated with BCX (r = 0.68) and proA (r = 0.98). However, no correlation was observed between proA and grain yield. Several hybrids with >10.0 t/ha grain yield with proA content >10.0 μg/g were identified. This is the first comprehensive study on development of diverse proA rich maize hybrids through marker-assisted pedigree breeding approach. The findings provides sustainable and cost-effective solution to alleviate vitamin-A deficiency.

135. GENOME-WIDE ASSOCIATION STUDY IDENTIFIES A LOCUS AT 7p15.2 ASSOCIATED WITH THE DEVELOPMENT OF MODERATE - SEVERE ENDOMETRIOSIS

2010 ◽  
Vol 22 (9) ◽  
pp. 53
Author(s):  
G. W. Montgomery ◽  
J. N. Painter ◽  
C. A. Anderson ◽  
D. R. Nyholt ◽  
S. Macgregor ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Severe Disease ◽  
Predictive Modelling ◽  
Genome Wide Association ◽  
Disease Stage ◽  
Genome Wide ◽  
A Genome ◽  
Variation Explained ◽  
The Uk

Endometriosis is a common gynaecological disease associated with severe pelvic pain and sub-fertility. There is considerable debate whether different endometriosis stages represent disease progression, or whether moderate-severe (rAFS III/IV) disease is pathological and minimal-mild (rAFS I/II) an epiphenomenon. We conducted a genome-wide association study using 540 082 SNPs in 3194 surgically confirmed endometriosis cases and 7060 controls from Australia and the UK. We used novel statistical methods to estimate the proportion of common variation explained by all markers and performed polygenic predictive modelling for disease stage, both showing significantly increased genetic loading among the 42% of cases with moderate-severe endometriosis. The strongest signals of association were also observed for moderate-severe disease. We subsequently genotyped 72 SNPs in an independent US dataset comprising 2392 endometriosis cases and 1646 controls. An association with rs7798431 on 7p15.2 for moderate-severe endometriosis (P = 6.0 × 10–8, OR = 1.34 (1.21–1.49)) was replicated, reaching combined genome-wide significance (P = 1.7 × 10–9; OR = 1.26 (1.17–1.35)). The implicated inter-genic region involves a 48 kb segment of high LD upstream of plausible candidate genes NFE2L3 and HOXA10. This locus is the first to be robustly implicated in the aetiology of endometriosis, with evidence of association limited to moderate-severe disease.

scholarly journals Whole-genome resequencing of Osmanthus fragrans provides insights into flower color evolution

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Hongguo Chen ◽  
Xiangling Zeng ◽  
Jie Yang ◽  
Xuan Cai ◽  
Yumin Shi ◽  
...  
Keyword(s):  
Genome Wide Association Study ◽  
Frameshift Mutation ◽  
Flower Color ◽  
Carotenoid Cleavage Dioxygenase ◽  
Coding Region ◽  
Osmanthus Fragrans ◽  
Floral Color ◽  
Regional Cluster ◽  
Population Structure Analysis ◽  
A Genome

AbstractOsmanthus fragrans is a well-known ornamental plant that has been domesticated in China for 2500 years. More than 160 cultivars have been found during this long period of domestication, and they have subsequently been divided into four cultivar groups, including the Yingui, Jingui, Dangui, and Sijigui groups. These groups provide a set of materials to study genetic evolution and variability. Here, we constructed a reference genome of O. fragrans ‘Liuyejingui’ in the Jingui group and investigated its floral color traits and domestication history by resequencing a total of 122 samples, including 119 O. fragrans accessions and three other Osmanthus species, at an average sequencing depth of 15×. The population structure analysis showed that these 119 accessions formed an apparent regional cluster. The results of linkage disequilibrium (LD) decay analysis suggested that varieties with orange/red flower color in the Dangui group had undergone more artificial directional selection; these varieties had the highest LD values among the four groups, followed by the Sijigui, Jingui, and Yingui groups. Through a genome-wide association study, we further identified significant quantitative trait loci and genomic regions containing several genes, such as ethylene-responsive transcription factor 2 and Arabidopsis pseudoresponse regulator 2, that are positively associated with petal color. Moreover, we found a frameshift mutation with a 34-bp deletion in the first coding region of the carotenoid cleavage dioxygenase 4 gene. This frameshift mutation existed in at least one site on both alleles in all varieties of the Dangui group. The results from this study shed light on the genetic basis of domestication in woody plants, such as O. fragrans.

scholarly journals Provitamin A Carotenoids in Baked Foods From Orange-Fleshed Sweet Potato Flour Are Substantially Bioaccessible and Contribute to Vitamin A Requirements

2020 ◽  
Vol 12 (10) ◽  
pp. 132
Author(s):  
Gisèle A. Koua ◽  
Sébastien Niamké
Keyword(s):  
Vitamin A ◽  
Sweet Potato ◽  
Vitamin A Deficiency ◽  
Public Health Problem ◽  
In Vitro Digestion ◽  
Provitamin A ◽  
Total Carotenoids ◽  
Provitamin A Carotenoids ◽  
Orange Fleshed Sweet Potato

Vitamin A deficiency (VAD) remains a public health problem in developing countries. Consumption of orange-fleshed sweet potato (OFSP) varieties has been proven to be a valuable strategy for VAD alleviation. In this work, OFSP flour was incorporated into wheat flour at 15, 25, 35, and 50% (w/w) and used to prepare baked products. The bioaccessibility of provitamin A carotenoids of OFSP baking products was performed according to an in vitro digestion model. The contribution of OFSP-wheat composite baking products to vitamin A requirements was evaluated. Relatively high amounts (98.70±2.17-144.42±1.31 μg/g DM) of total carotenoids in OFSP flours was reported in Kakamega-7-Irene, Kabode, and Covington cultivars. The recovery of provitamin A carotenoid in baking products containing 15, 25, 35, and 50% OFSP flour was 1031.04±6.36-3364.21±10.22 μg/100 g for cupcakes and 1009.19±10.38-4640.72±13.43 μg/100 g for cookies, respectively. The in vitro bioaccessibility of provitamin A carotenoids of OFSP composite cupcake ranged from 12.53 to 27.21% while that of OFSP composite cookies was significantly different (p ˂ 0.05) and ranged from 15.99 to 27.84%. The results also showed that cupcake and cookies containing 35% and 50% OFSP flours could be used to fight vitamin A deficiency in Côte d’Ivoire as they were found to meet 50 and more than 100% (161% for 100 g portion) of the recommended dietary allowance (RDA) of vitamin A for children aged 3-10 years. Finally, our results may support adoption of OFSP varieties in order to decrease the risk of vitamin A deficiency in Côte d’Ivoire.

scholarly journals Joint sequencing of human and pathogen genomes reveals the genetics of pneumococcal meningitis

2018 ◽  
Author(s):  
John A. Lees ◽  
Bart Ferwerda ◽  
Philip H. C. Kremer ◽  
Nicole E. Wheeler ◽  
Mercedes Valls Serón ◽  
...  
Keyword(s):  
Pneumococcal Disease ◽  
Pneumococcal Meningitis ◽  
Genome Wide Association Study ◽  
Interaction Analysis ◽  
Invasive Potential ◽  
Genome Wide ◽  
A Genome ◽  
Invasive Diseases ◽  
Life Threatening ◽  
Variation Explained

AbstractStreptococcus pneumoniae is a common nasopharyngeal colonizer, but can also cause life-threatening invasive diseases such as empyema, bacteremia and meningitis. Genetic variation of host and pathogen is known to play a role in invasive pneumococcal disease, though to what extent is unknown. In a genome-wide association study of human and pathogen we show that human variation explains almost half of variation in susceptibility to pneumococcal meningitis and one-third of variation in severity, and identified variants in CCDC33 associated with susceptibility. Pneumococcal variation explained a large amount of invasive potential, but serotype explained only half of this variation. Newly developed methods identified pneumococcal genes involved in invasiveness including pspC and zmpD, and allowed a human-bacteria interaction analysis, finding associations between pneumococcal lineage and STK32C.

scholarly journals Analysis of coding variants in the human FTO gene from the ExAC (gnomAD) Database

2021 ◽  
Author(s):  
Mauro Lúcio Ferreira Souza ◽  
Jaime Viana de Sousa ◽  
João Farias Guerreiro
Keyword(s):  
Genome Wide Association Study ◽  
Rare Variants ◽  
Human Populations ◽  
Nucleotide Polymorphisms ◽  
Fto Gene ◽  
Low Frequencies ◽  
Functional Variants ◽  
Pathogenicity Prediction ◽  
A Genome ◽  
Coding Variants

AbstractSingle nucleotide polymorphisms (SNPs) in the first intron of the FTO gene (alpha-ketoglutarate-dependent dioxygenase) identified by a genome-wide association study (GWAS) in 2007 continue to be the known variants with the greatest effect on adiposity in different human populations. Currently available data reveal a total of 61 different intronic SNPs associated with adiposity. Coding variants in the FTO gene, on the other hand, have been little explored, but data from complete sequencing of the exomes of various populations are available in public databases and provide an excellent opportunity to investigate potential functional variants in FTO. This study aimed to track nonsynonymous variants in the exons of the FTO gene in different population groups using the ExAC database (gnomAD) (http://exac.broadinstitute.org/) and to analyze the potential functional impact of these variants on the FTO protein. Variants were analyzed using five publicly available pathogenicity prediction programs. Of the 158 mutations identified (152 missense and 6 stop-gain), 64 (40.5%) were classified as pathogenic, 67 (42.4%) were classified as benign, and 27 (17%) were classified as inconclusive. Thirty variants were classified as pathogenic by all five predictors used in this study, and 16 mutations were classified as pathogenic by only one predictor. The largest number of mutations was found in Europeans (non-Finnish) (85/158), all with very low frequencies, and half (32/64) of the variants classified as pathogenic by the five predictors used were also found in this population. The data obtained in this analysis show that a large number of rare coding variants classified as pathogenic or potentially pathogenic by different in silico pathogenicity prediction programs are not detected by GWAS due to the low linkage disequilibrium as well as the limitations of GWAS in capturing rare variants present in less than 1.0% of the population.

scholarly journals Carotenoid content of pandanus fruit cultivars and other foods of the Republic of Kiribati

2006 ◽  
Vol 9 (5) ◽  
pp. 631-643 ◽  
Author(s):  
Lois Englberger ◽  
William Aalbersberg ◽  
Usaia Dolodolotawake ◽  
Joseph Schierle ◽  
Julia Humphries ◽  
...  
Keyword(s):  
Vitamin A ◽  
High Performance ◽  
Vitamin A Deficiency ◽  
Analytical Techniques ◽  
Provitamin A ◽  
Carotenoid Content ◽  
Total Carotenoids ◽  
Potential Health ◽  
The Pacific ◽  
Indigenous Foods

AbstractBackgroundKiribati, a remote atoll island country of the Pacific, has serious problems of vitamin A deficiency (VAD). Thus, it is important to identify locally grown acceptable foods that might be promoted to alleviate this problem. Pandanus fruit (Pandanus tectorius) is a well-liked indigenous Kiribati food with many cultivars that have orange/yellow flesh, indicative of carotenoid content. Few have been previously analysed.AimThis study was conducted to identify cultivars of pandanus and other foods that could be promoted to alleviate VAD in Kiribati.MethodEthnography was used to select foods and assess acceptability factors. Pandanus and other foods were analysed for β- and α-carotene, β-cryptoxanthin, lutein, zeaxanthin, lycopene and total carotenoids using high-performance liquid chromatography.ResultsOf the nine pandanus cultivars investigated there was a great range of provitamin A carotenoid levels (from 62 to 19 086 μg β-carotene/100 g), generally with higher levels in those more deeply coloured. Seven pandanus cultivars, one giant swamp taro (Cyrtosperma chamissonis) cultivar and native fig (Ficus tinctoria) had significant provitamin A carotenoid content, meeting all or half of estimated daily vitamin A requirements within normal consumption patterns. Analyses in different laboratories confirmed high carotenoid levels in pandanus but showed that there are still questions as to how high the levels might be, owing to variation arising from different handling/preparation/analytical techniques.ConclusionsThese carotenoid-rich acceptable foods should be promoted for alleviating VAD in Kiribati and possibly other Pacific contexts where these foods are important. Further research in the Pacific is needed to identify additional indigenous foods with potential health benefits.

scholarly journals Genomic Association vs. Serological Determination of ABO Blood Types in a Chinese Cohort, with Application in Mendelian Randomization

Genes ◽  
2021 ◽  
Vol 12 (7) ◽  
pp. 959
Author(s):  
Mengqiao Wang ◽  
Jiaqi Gao ◽  
Jin Liu ◽  
Xing Zhao ◽  
Yi Lei
Keyword(s):  
Genetic Variants ◽  
Genome Wide Association Study ◽  
Linear Models ◽  
Mendelian Randomization ◽  
Human Populations ◽  
Nucleotide Polymorphisms ◽  
A Genome ◽  
Genomic Association ◽  
Multi Class Classification ◽  
Log Linear

ABO blood system is an inborn trait determined by the ABO gene. The genetic-phenotypic mechanism underneath the four mutually exclusive and collectively exhaustive types of O, A, B and AB could theoretically be elucidated. However, genetic polymorphisms in the human populations render the link elusive, and importantly, past studies using genetically determined rather than biochemically determined ABO types were not and could not be evaluated for the inference errors. Upon both blood-typing and genotyping a cohort of 1008 people of the Han Chinese population, we conducted a genome-wide association study in parallel with both binomial and multinomial log-linear models. Significant genetic variants are all mapped to the ABO gene, and are quantitatively evaluated for binary and multi-class classification performances. Three single nucleotide polymorphisms of rs8176719, rs635634 and rs7030248 would together be sufficient to establish a multinomial predictive model that achieves high accuracy (0.98) and F1 scores (micro 0.99 and macro 0.97). Using the set of identified ABO-associated genetic variants as instrumental variables, we demonstrate the application in causal analysis by Mendelian randomization (MR) studies on blood pressures (one-sample MR) and severe COVID-19 with respiratory failure (two-sample MR).

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