scholarly journals Comparative Assessment of Effectiveness of Alternative Genotyping Assays for Characterizing Carotenoids Accumulation in Tropical Maize Inbred Lines

Agronomy ◽  
2021 ◽  
Vol 11 (10) ◽  
pp. 2022
Author(s):  
Abdoul-Raouf Sayadi Maazou ◽  
Melaku Gedil ◽  
Victor O. Adetimirin ◽  
Silvestro Meseka ◽  
Wende Mengesha ◽  
...  
Keyword(s):  
Vitamin A Deficiency ◽  
Inbred Lines ◽  
Provitamin A ◽  
Carotenoid Content ◽  
Functional Markers ◽  
Favorable Alleles ◽  
Specific Pcr ◽  
Maize Inbred Lines ◽  
Maize Varieties ◽  
Allele Specific

The development of maize varieties with increased concentration of Provitamin A (PVA) is an effective and affordable strategy to combat vitamin A deficiency in developing nations. However, the considerably high cost of carotene analysis poses a major challenge for maize PVA biofortification, prompting the use of marker-assisted selection. Presently, two types of genotyping with PVA trait-linked functional markers have been developed and extensively used in breeding programs. The two systems are low throughput gel-based genotyping and genotyping with Kompetitive Allele-Specific PCR (KASP) single nucleotide polymorphism (SNPs) markers. Although the KASP SNPs genotyping was developed to replace the gel-based genotyping, studies have not been conducted to compare the effectiveness of the KASP SNPs markers with the gel-based markers. This study was conducted to assess the carotenoid content of 64 tropical PVA biofortified maize inbred lines containing temperate germplasm in their genetic backgrounds and screen them with both gel-based and KASP markers of PSY1, LCYE and crtRB1 genes. Many of the 64 inbred lines had PVA concentrations surpassing the 15 µg/g provitamin A breeding target set by the HarvestPlus Challenge Program. Favorable alleles of crtRB1, crtRB1 and the KASP SNPs markers were detected in 25 inbred lines with high PVA concentrations. Inbred lines with the favorable alleles of LCYE had the highest concentrations of non-PVA carotenoids, whereas those with the favorable alleles of crtRB1 had high levels of PVA carotenoids. Data from the sequenced region of LCYE revealed one SNP in the first intron that clearly differentiated the high and low β-carotene maize inbred lines. The results of our study demonstrate that the automated KASP SNPs markers can replace the gel-based genotyping for screening a large number of early generation maize inbred lines for PVA content.

scholarly journals Development of genic KASP SNP markers from RNA-Seq data for map-based cloning and marker-assisted selection in maize

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Zhengjie Chen ◽  
Dengguo Tang ◽  
Jixing Ni ◽  
Peng Li ◽  
Le Wang ◽  
...  
Keyword(s):  
Marker Assisted Selection ◽  
Inbred Lines ◽  
Average Density ◽  
Snp Markers ◽  
Data Sets ◽  
Rna Seq ◽  
Specific Pcr ◽  
Maize Inbred Lines ◽  
Allele Specific ◽  
Allele Specific Pcr

Abstract Background Maize is one of the most important field crops in the world. Most of the key agronomic traits, including yield traits and plant architecture traits, are quantitative. Fine mapping of genes/ quantitative trait loci (QTL) influencing a key trait is essential for marker-assisted selection (MAS) in maize breeding. However, the SNP markers with high density and high polymorphism are lacking, especially kompetitive allele specific PCR (KASP) SNP markers that can be used for automatic genotyping. To date, a large volume of sequencing data has been produced by the next generation sequencing technology, which provides a good pool of SNP loci for development of SNP markers. In this study, we carried out a multi-step screening method to identify kompetitive allele specific PCR (KASP) SNP markers based on the RNA-Seq data sets of 368 maize inbred lines. Results A total of 2,948,985 SNPs were identified in the high-throughput RNA-Seq data sets with the average density of 1.4 SNP/kb. Of these, 71,311 KASP SNP markers (the average density of 34 KASP SNP/Mb) were developed based on the strict criteria: unique genomic region, bi-allelic, polymorphism information content (PIC) value ≥0.4, and conserved primer sequences, and were mapped on 16,161 genes. These 16,161 genes were annotated to 52 gene ontology (GO) terms, including most of primary and secondary metabolic pathways. Subsequently, the 50 KASP SNP markers with the PIC values ranging from 0.14 to 0.5 in 368 RNA-Seq data sets and with polymorphism between the maize inbred lines 1212 and B73 in in silico analysis were selected to experimentally validate the accuracy and polymorphism of SNPs, resulted in 46 SNPs (92.00%) showed polymorphism between the maize inbred lines 1212 and B73. Moreover, these 46 polymorphic SNPs were utilized to genotype the other 20 maize inbred lines, with all 46 SNPs showing polymorphism in the 20 maize inbred lines, and the PIC value of each SNP was 0.11 to 0.50 with an average of 0.35. The results suggested that the KASP SNP markers developed in this study were accurate and polymorphic. Conclusions These high-density polymorphic KASP SNP markers will be a valuable resource for map-based cloning of QTL/genes and marker-assisted selection in maize. Furthermore, the method used to develop SNP markers in maize can also be applied in other species.

scholarly journals Assessing Effect of Marker-Based Improvement of Maize Synthetics on Agronomic Performance, Carotenoid Content, Combining Ability and Heterosis

Agronomy ◽  
2020 ◽  
Vol 10 (11) ◽  
pp. 1625
Author(s):  
Innocent Iseghohi ◽  
Ayodeji Abe ◽  
Silvestro Meseka ◽  
Wende Mengesha ◽  
Melaku Gedil ◽  
...  
Keyword(s):  
Grain Yield ◽  
Agronomic Traits ◽  
Vitamin A Deficiency ◽  
Inbred Lines ◽  
Provitamin A ◽  
Carotenoid Content ◽  
Agronomic Performance ◽  
Gene Effects ◽  
Additive Gene ◽  
Β Carotene

Vitamin A deficiency (VAD) is a serious problem in sub-Saharan Africa (SSA) and other parts of the world. Understanding the effect of marker-based improvement (MARS) of two maize synthetics (HGA and HGB) representing different heterotic groups on their agronomic performance, carotenoid content, and combining abilities could help identify suitable sources to develop divergent inbred lines for optimizing heterosis. This study involved three selection cycles each of the two synthetics and their nine varietal-cross hybrids together with a released check variety was conducted across four diverse locations in Nigeria in 2018 and 2019. Environment and hybrid effects were significant on grain yield and other agronomic traits as well as provitamin A content and other carotenoids. Genetic improvement per cycle of MARS in the parental synthetics was 15% for provitamin A, 25% for β-carotene and 26% for lutein in HGA and 4% for grain yield, 3% for zeaxanthin and 5% for α-carotene in HGB. Grain yield and agronomic traits of the two maize synthetics were controlled by additive and non-additive gene effects, while provitamin A content and other carotenoids were mainly controlled by additive gene effects. Some selection cycles which were high in grain yield and provitamin A content were identified as potential sources of new and divergent maize inbred lines in maize breeding programs. Some varietal-cross hybrids expressed significant mid-parent heterosis for grain yield and moderate mid-parent heterosis for provitamin A, β-carotene and xanthophylls. These hybrids could be commercialized at reasonable prices to small-scale farmers in rural areas that are most affected by vitamin A deficiency.

scholarly journals Combining Ability and Heterosis for Endosperm Carotenoids and Agronomic Traits in Tropical Maize Lines

2021 ◽  
Vol 12 ◽  
Author(s):  
Girum Azmach ◽  
Melaku Gedil ◽  
Charles Spillane ◽  
Abebe Menkir
Keyword(s):  
Combining Ability ◽  
Agronomic Traits ◽  
Vitamin A Deficiency ◽  
Public Health Problem ◽  
Inbred Lines ◽  
Provitamin A ◽  
F1 Hybrids ◽  
Carotenoid Content ◽  
Gene Effects ◽  
Gxe Interaction

Provitamin A enrichment of staple crops through biofortification breeding is a powerful approach to mitigate the public health problem of vitamin A deficiency in developing countries. Twenty-four genetically diverse yellow and orange endosperm maize inbred lines with differing levels of provitamin A content were used for the analysis of their combining ability. Each inbred line was developed from crosses and backcrosses between temperate and tropical germplasm. The inbred lines were grouped into different sets according to their provitamin A levels and were then intercrossed in a factorial mating scheme to generate 80 different single-cross hybrids. The hybrids were evaluated in field trials across a range of agroecological zones in Nigeria. The effect of hybrids was significant on all the measured provitamin A and non-provitamin A carotenoids and agronomic traits. While the effect of genotype-by-environment (GxE) interaction was significant for almost all traits, it was a non-crossover-type interaction for carotenoid content. Partitioning of the variances associated with the carotenoid and agronomic traits into their respective components revealed the presence of significant positive and negative estimates of general combining ability (GCA) and specific combining ability (SCA) effects for both carotenoid content and agronomic traits. The preponderance of GCA effects indicates the importance of additive gene effects in the inheritance of carotenoid content. We found F1 hybrids displaying high parent heterosis for both provitamin A content and agronomic performance. Our study demonstrates that provitamin A biofortification can be effectively implemented in maize breeding programs without adverse effects on important agronomic traits, including grain yield.

scholarly journals Allelic polymorphism of crtRB1 and LcyE genes related to the β-carotene content in Vietnamese traditional maize accessions,

2019 ◽  
Vol 41 (3) ◽  
Author(s):  
Nguyen Duc Thanh ◽  
Nguyen Thi Lan ◽  
Ho Thi Huong
Keyword(s):  
Animal Feed ◽  
Genetic Research ◽  
Provitamin A ◽  
Carotenoid Content ◽  
Allelic Polymorphism ◽  
Allele Polymorphism ◽  
Carotene Content ◽  
Favorable Alleles ◽  
Maize Varieties ◽  
Β Carotene

Maize is the third most important food crop after wheat and rice. Maize is used as food for more than a billion people around the world and is used as animal feed, especially, poultry. The concentration of carotenoids, especially, β-carotene in maize grains, is very low. Therefore, the study of increasing the amount of provitamin A carotenoids including β-carotene is important. In maize, different alleles of crtRB1 and LcyE genes have a significant effect on β-carotene content. In this paper, we present the results of the study of allele polymorphism of these two genes related to the provitamin A carotenoid content in some traditional maize accessions collected from several regions in North and Central Highlands of Vietnam. The results showed that there were polymorphisms at the 3’ and 5’ ends of the crtRB1 and LcyE genes. Among 22 maize accessions, the proportion of favorable alleles at the 3’ end of crtRB1 gene was relatively high (5/22 = 22.73%). Similar results were obtained for alleles at 3’ end of the LcyE gene. Especially, there is an accession (Northern white gold maize) that carries favorable alleles at the 3’ ends of both crtRB1 and LcyE genes. While all investigated maize accessions did not carry favorable alleles at the 5’ end of both crtRB1 and LcyE genes. The identification of traditional maize accessions that carry favorable alleles for increasing b-carotene content opens up potential to exploit indigenous genetic resources for genetic research as well as to develop maize varieties with high β- carotene content. 

SSR-based and carotenoid diversity assessment of tropical yellow endosperm maize inbred lines

2013 ◽  
Vol 12 (1) ◽  
pp. 67-73 ◽  
Author(s):  
Oyenike Adeyemo ◽  
Olusesan Omidiji
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Polymorphic Information Content ◽  
Vitamin A Deficiency ◽  
Inbred Lines ◽  
Reproductive Age ◽  
Sub Saharan Africa ◽  
Provitamin A ◽  
Maize Inbred Lines ◽  
Diversity Assessment

Yellow endosperm maize can be used to reduce vitamin A deficiency among many pre-school children and women of reproductive age in sub-Saharan Africa. Assessment of the genetic diversity of tropical yellow endosperm maize inbred lines will have genetic gains in breeding design to develop lines with an enhanced level of provitamin A. We screened 122 tropical yellow endosperm maize inbred lines with 62 simple sequence repeat (SSR) markers and 51 SSR loci were polymorphic. We detected 190 alleles with an average of 3.72 alleles per locus, and polymorphic information content values among the inbred lines varied from 0.12 to 0.74 with an average of 0.43. Genetic distance (GD) values among all the pairs of the 122 inbred lines varied from 0.02 to 0.61 with an average of 0.41 for the SSR markers. The inbred lines exhibited a substantial level of genetic diversity. Genetic diversity was also evaluated using carotenoid data. The Euclidean GDs varied from 1.00 to 9.97 with an average of 3.81 for the carotenoid data. Cluster and principal coordinate analyses revealed clear separation of maize inbred lines into SSR-based groupings and carotenoid-based groupings. Cluster based on SSR markers were predominantly consistent with known pedigree data of the inbred lines. The correlation using Mantel's test between carotenoid-based GD estimates and SSR marker-based GD estimates gave a low r value ( − 0.06). The grouping of lines will facilitate the selection of parental lines for making crosses to develop new lines with enhanced provitamin A content.

scholarly journals Allelic polymorphism of crtRB1 and LcyE genes related to the β-carotene content in Vietnamese traditional maize accessions,

2019 ◽  
Vol 41 (3) ◽  
Author(s):  
Nguyen Duc Thanh ◽  
Nguyen Thi Lan ◽  
Ho Thi Huong
Keyword(s):  
Animal Feed ◽  
Genetic Research ◽  
Provitamin A ◽  
Carotenoid Content ◽  
Allelic Polymorphism ◽  
Allele Polymorphism ◽  
Carotene Content ◽  
Favorable Alleles ◽  
Maize Varieties ◽  
Β Carotene

Maize is the third most important food crop after wheat and rice. Maize is used as food for more than a billion people around the world and is used as animal feed, especially, poultry. The concentration of carotenoids, especially, β-carotene in maize grains, is very low. Therefore, the study of increasing the amount of provitamin A carotenoids including β-carotene is important. In maize, different alleles of crtRB1 and LcyE genes have a significant effect on β-carotene content. In this paper, we present the results of the study of allele polymorphism of these two genes related to the provitamin A carotenoid content in some traditional maize accessions collected from several regions in North and Central Highlands of Vietnam. The results showed that there were polymorphisms at the 3’ and 5’ ends of the crtRB1 and LcyE genes. Among 22 maize accessions, the proportion of favorable alleles at the 3’ end of crtRB1 gene was relatively high (5/22 = 22.73%). Similar results were obtained for alleles at 3’ end of the LcyE gene. Especially, there is an accession (Northern white gold maize) that carries favorable alleles at the 3’ ends of both crtRB1 and LcyE genes. While all investigated maize accessions did not carry favorable alleles at the 5’ end of both crtRB1 and LcyE genes. The identification of traditional maize accessions that carry favorable alleles for increasing b-carotene content opens up potential to exploit indigenous genetic resources for genetic research as well as to develop maize varieties with high β- carotene content. 

scholarly journals Two User-Friendly Molecular Markers Developed for the Identification of Hybrid Lethality Genes in Brassica oleracea

Agronomy ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 982
Author(s):  
Zhiliang Xiao ◽  
Congcong Kong ◽  
Fengqing Han ◽  
Limei Yang ◽  
Mu Zhuang ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Brassica Oleracea ◽  
Rapid Identification ◽  
Inbred Lines ◽  
Hybrid Lethality ◽  
Specific Pcr ◽  
Allele Specific ◽  
User Friendly ◽  
Allele Specific Pcr ◽  
Kasp Marker

Cabbage (Brassica oleracea) is an important vegetable crop that is cultivated worldwide. Previously, we reported the identification of two dominant complementary hybrid lethality (HL) genes in cabbage that could result in the death of hybrids. To avoid such losses in the breeding process, we attempted to develop molecular markers to identify HL lines. Among 54 previous mapping markers closely linked to BoHL1 or BoHL2, only six markers for BoHL2 were available in eight cabbage lines (two BoHL1 lines; three BoHL2 lines; three lines without BoHL); however, they were neither universal nor user-friendly in more inbred lines. To develop more accurate markers, these cabbage lines were resequenced at an ~20× depth to obtain more nucleotide variations in the mapping regions. Then, an InDel in BoHL1 and a single-nucleotide polymorphism (SNP) in BoHL2 were identified, and the corresponding InDel marker MBoHL1 and the competitive allele-specific PCR (KASP) marker KBoHL2 were developed and showed 100% accuracy in eight inbred lines. Moreover, we identified 138 cabbage lines using the two markers, among which one inbred line carried BoHL1 and 11 inbred lines carried BoHL2. All of the lethal line genotypes obtained with the two markers matched the phenotype. Two markers were highly reliable for the rapid identification of HL genes in cabbage.

scholarly journals Cassava with enhanced β-carotene maintains adequate vitamin A status in Mongolian gerbils (Meriones unguiculatus) despite substantial cis-isomer content

2009 ◽  
Vol 102 (3) ◽  
pp. 342-349 ◽  
Author(s):  
Julie A. Howe ◽  
Bussie Maziya-Dixon ◽  
Sherry A. Tanumihardjo
Keyword(s):  
Vitamin A ◽  
Vitamin A Deficiency ◽  
Meriones Unguiculatus ◽  
Provitamin A ◽  
Carotenoid Content ◽  
Mongolian Gerbils ◽  
Serum Retinol ◽  
Vitamin A Status ◽  
Isomer Content ◽  
Β Carotene

Efforts to increase β-carotene in cassava have been successful, but the ability of high-β-carotene cassava to prevent vitamin A deficiency has not been determined. Two studies investigated the bioefficacy of provitamin A in cassava and compared the effects of carotenoid content and variety on vitamin A status in vitamin A-depleted Mongolian gerbils (Meriones unguiculatus). Gerbils were fed a vitamin A-free diet 4 weeks prior to treatment. In Expt 1, treatments (ten gerbils per group) included 45 % high-β-carotene cassava, β-carotene and vitamin A supplements (intake matched to high-β-carotene cassava group), and oil control. In Expt 2, gerbils were fed cassava feeds with 1·8 or 4·3 nmol provitamin A/g prepared with two varieties. Gerbils were killed after 4 weeks. For Expt 1, liver vitamin A was higher (P < 0·05) in the vitamin A (1·45 (sd 0·23) μmol/liver), lower in the control (0·43 (sd 0·10) μmol/liver), but did not differ from the β-carotene group (0·77 (sd 0·12) μmol/liver) when compared with the high-β-carotene cassava group (0·69 (sd 0·20) μmol/liver). The bioconversion factor was 3·7 μg β-carotene to 1 μg retinol (2 mol:1 mol), despite 48 % cis-β-carotene [(Z)-β-carotene] composition in cassava. In Expt 2, cassava feed with 4·3 nmol provitamin A/g maintained vitamin A status. No effect of cassava variety was observed. Serum retinol concentrations did not differ. β-Carotene was detected in livers of gerbils receiving cassava and supplements, but the cis-to-trans ratio in liver differed from intake. Biofortified cassava adequately maintained vitamin A status and was as efficacious as β-carotene supplementation in the gerbil model.

Erratum to: Progress and perspectives for carotenoid accumulation in selected Triticeae species

2011 ◽  
Vol 62 (6) ◽  
pp. 531
Author(s):  
C. Rodríguez-Suárez ◽  
M. J. Giménez ◽  
S. G. Atienza
Keyword(s):  
Human Health ◽  
Vitamin A Deficiency ◽  
Carotenoid Content ◽  
Functional Markers ◽  
Relevant Issue ◽  
Health And Nutrition ◽  
Triticeae Species ◽  
Total Carotenoid Content ◽  
Carotenogenic Genes ◽  
Breeding Target

Plant carotenoids are C40 isoprenoids with multiple biological roles. Breeding for carotenoid content in rice, maize and wheat is a relevant issue, both for their importance in human health and nutrition and for their influence in food colouration in products such as pasta from durum wheat. Regarding human health, vitamin A deficiency (VAD) is one of the major causes of malnutrition in the world. As many as 500�000 children become blind due to VAD each year with many of them dying from VAD-related illness within 1 year. This review presents the main results in the improvement of endosperm carotenoid levels in rice, maize and wheat considering the methodology used, either transgenic or non-transgenic; the breeding target, such as provitamin A or total carotenoid content; the identification of new carotenogenic genes/alleles related to the available variation for this trait; and the development of new functional markers for marker-assisted selection. A comparative overview among these species and key areas for further improvement are also identified. Carotenoid enhancement in grasses would benefit from comparative studies among Triticeae species since they allow the understanding of the diversity basis. Therefore, the comparative overview given in this work will be relevant not only to rice, maize and wheat but also to other Triticeae species.

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