Genetic dissection of grain iron and zinc, and thousand kernel weight in wheat (Triticum aestivum L.) using genome-wide association study

Krishnappa, Gopalareddy; Khan, Hanif; Krishna, Hari; Kumar, Satish; Mishra, Chandra Nath; Devate, Narayana Bhat; Nepolean, Thirunavukkarasu; Rathan, Nagenahalli Dharmegowda; Mamrutha, H. M.; Srivastava, Puja; Biradar, Suma; Uday, G.; Kumar, M. B. Arun; Singh, Gyanendra

doi:10.1038/s41598-022-15992-z

Cited by 23 publications

(26 citation statements)

References 87 publications

(127 reference statements)

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“…However, the correlation between TKW and all the three agro-morphological traits was significant and highly negative, except in Y3 for PH. Significant correlations found in this study have also been reported in earlier studies [ 23 , 42 ]. The positively associated traits (DH, DM, and PH) can be improved simultaneously; however, for the improvement of negatively associated traits, the adoption of suitable breeding-methods to break the undesirable linkages is envisaged.…”

Section: Discussionsupporting

confidence: 91%

“…Eight QTLs were identified for TKW on the 3A, 4A, 5A, 5B, 6A, and 7D chromosomes. Previous reports also identified some QTLs on the same chromosomes: 3A [ 10 , 19 , 24 , 50 , 56 ], 4A [ 19 , 31 , 46 , 50 ], 5A [ 23 , 29 , 40 , 57 ], 5B [ 20 , 29 , 40 , 45 , 52 , 53 , 54 , 57 ], 6A [ 23 , 29 , 31 , 37 , 46 , 48 , 50 , 52 , 53 , 55 , 56 , 57 ], and 7D [ 29 , 31 , 40 , 50 ], at different positions. In addition, three previous reports, i.e., Gahlaut et al [ 19 ], Edae et al [ 46 ], and Ramya et al [ 27 ] identified a QTL at 73 cM, 72.4 cM, and 70 cM, respectively, on the 5B chromosome, which was similar to the QTL ( QTKW-5B ) identified in the present study at 70.5–73.5 cM, on the same chromosome.…”

Section: Discussionmentioning

confidence: 97%

“…Genome-wide association studies (GWAS) and quantitative-trait-loci (QTL) mapping are the two widely used methods to dissect the genetic basis of complex quantitative traits in crop plants. In previous studies, GWAS panels have been phenotyped in a range of production conditions including drought, irrigated, heat, salt stress, and different nitrogen regimes, to identify QTLs associated with grain yield and its contributing traits through GWAS [ 10 , 18 , 19 , 20 , 21 , 22 , 23 , 24 , 25 ]. Similarly, several QTLs associated with yield and contributing traits have been identified through bi-parental populations-based QTL mapping under diverse production conditions (irrigated, drought, heat, organic) and different genetic backgrounds (synthetic wheat, Rye selections or translocations, non-adapted background) [ 26 , 27 , 28 , 29 , 30 , 31 , 32 , 33 , 34 ].…”

Section: Introductionmentioning

confidence: 99%

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Mapping QTL for Phenological and Grain-Related Traits in a Mapping Population Derived from High-Zinc-Biofortified Wheat

Rathan

Krishnappa

Singh

et al. 2023

Plants

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Genomic regions governing days to heading (DH), days to maturity (DM), plant height (PH), thousand-kernel weight (TKW), and test weight (TW) were investigated in a set of 190 RILs derived from a cross between a widely cultivated wheat-variety, Kachu (DPW-621-50), and a high-zinc variety, Zinc-Shakti. The RIL population was genotyped using 909 DArTseq markers and phenotyped in three environments. The constructed genetic map had a total genetic length of 4665 cM, with an average marker density of 5.13 cM. A total of thirty-seven novel quantitative trait loci (QTL), including twelve for PH, six for DH, five for DM, eight for TKW and six for TW were identified. A set of 20 stable QTLs associated with the expression of DH, DM, PH, TKW, and TW were identified in two or more environments. Three novel pleiotropic genomic-regions harboring co-localized QTLs governing two or more traits were also identified. In silico analysis revealed that the DArTseq markers were located on important putative candidate genes such as MLO-like protein, Phytochrome, Zinc finger and RING-type, Cytochrome P450 and pentatricopeptide repeat, involved in the regulation of pollen maturity, the photoperiodic modulation of flowering-time, abiotic-stress tolerance, grain-filling duration, thousand-kernel weight, seed morphology, and plant growth and development. The identified novel QTLs, particularly stable and co-localized QTLs, will be validated to estimate their effects in different genetic backgrounds for subsequent use in marker-assisted selection (MAS).

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Section: Discussionsupporting

confidence: 91%

Section: Discussionmentioning

confidence: 97%

Section: Introductionmentioning

confidence: 99%

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Mapping QTL for Phenological and Grain-Related Traits in a Mapping Population Derived from High-Zinc-Biofortified Wheat

Rathan

Krishnappa

Singh

et al. 2023

Plants

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“…QTLs with large effects were detected on chromosomes 2B and 7B and are associated with transcription factors such as zinc finger motifs and metal ion binding protein (phosphatase), all of which has a role in the additional loading of Zn in wheat grains. Multiple studies have reported QTLs for high Zn and Fe concentrations on chromosomes 2A, 2B, 5A, and 7B ( Srinivasa et al, 2014 ; Alomari et al, 2018 ; Alomari et al, 2019 ; Krishnappa et al, 2022 ). Transfer of these QTLs through marker assisted breeding will certainly improve mineral concentrations in wheat grains.…”

Section: Breeding For Improved Grain Zinc and Iron Content In Wheatmentioning

confidence: 99%

Genomic approaches for improving grain zinc and iron content in wheat

Roy

Kumar²,

Ranjan³

et al. 2022

Front. Genet.

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More than three billion people worldwide suffer from iron deficiency associated anemia and an equal number people suffer from zinc deficiency. These conditions are more prevalent in Sub-Saharan Africa and South Asia. In developing countries, children under the age of five with stunted growth and pregnant or lactating women were found to be at high risk of zinc and iron deficiencies. Biofortification, defined as breeding to develop varieties of staple food crops whose grain contains higher levels of micronutrients such as iron and zinc, are one of the most promising, cost-effective and sustainable ways to improve the health in resource-poor households, particularly in rural areas where families consume some part of what they grow. Biofortification through conventional breeding in wheat, particularly for grain zinc and iron, have made significant contributions, transferring important genes and quantitative trait loci (QTLs) from wild and related species into cultivated wheat. Nonetheless, the quantitative, genetically complex nature of iron and zinc levels in wheat grain limits progress through conventional breeding, making it difficult to attain genetic gain both for yield and grain mineral concentrations. Wheat biofortification can be achieved by enhancing mineral uptake, source-to-sink translocation of minerals and their deposition into grains, and the bioavailability of the minerals. A number of QTLs with major and minor effects for those traits have been detected in wheat; introducing the most effective into breeding lines will increase grain zinc and iron concentrations. New approaches to achieve this include maker assisted selection and genomic selection. Faster breeding approaches need to be combined to simultaneously increase grain mineral content and yield in wheat breeding lines.

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“…Agronomic biofortification is based on optimized fertilizer applications, whereas genetic biofortification is based on traditional plant breeding and/or genetic engineering to improve nutrient concentrations ( Cakmak, 2008 ; Borrill et al., 2014 ). Out of these two strategies, genetic biofortification has been identified as an effective and affordable technique to enhance food nutrition content in a sustainable long-lasting way to combat mineral nutrition deficiencies ( Krishnappa et al., 2022 ).…”

Section: Introductionmentioning

confidence: 99%

Genetic dissection of marker trait associations for grain micro-nutrients and thousand grain weight under heat and drought stress conditions in wheat

et al. 2023

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IntroductionWheat is grown and consumed worldwide, making it an important staple food crop for both its calorific and nutritional content. In places where wheat is used as a staple food, suboptimal micronutrient content levels, especially of grain iron (Fe) and zinc (Zn), can lead to malnutrition. Grain nutrient content is influenced by abiotic stresses, such as drought and heat stress. The best method for addressing micronutrient deficiencies is the biofortification of food crops. The prerequisites for marker-assisted varietal development are the identification of the genomic region responsible for high grain iron and zinc contents and an understanding of their genetics.MethodsA total of 193 diverse wheat genotypes were evaluated under drought and heat stress conditions across the years at the Indian Agricultural Research Institute (IARI), New Delhi, under timely sown irrigated (IR), restricted irrigated (RI) and late sown (LS) conditions. Grain iron content (GFeC) and grain zinc content (GZnC) were estimated from both the control and treatment groups. Genotyping of all the lines under study was carried out with the single nucleotide polymorphisms (SNPs) from Breeder’s 35K Axiom Array.Result and DiscussionThree subgroups were observed in the association panel based on both principal component analysis (PCA) and dendrogram analysis. A large whole-genome linkage disequilibrium (LD) block size of 3.49 Mb was observed. A genome-wide association study identified 16 unique stringent marker trait associations for GFeC, GZnC, and 1000-grain weight (TGW). In silico analysis demonstrated the presence of 28 potential candidate genes in the flanking region of 16 linked SNPs, such as synaptotagmin-like mitochondrial-lipid-binding domain, HAUS augmin-like complex, di-copper center-containing domain, protein kinase, chaperonin Cpn60, zinc finger, NUDIX hydrolase, etc. Expression levels of these genes in vegetative tissues and grain were also found. Utilization of identified markers in marker-assisted breeding may lead to the rapid development of biofortified wheat genotypes to combat malnutrition.

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Genetic dissection of grain iron and zinc, and thousand kernel weight in wheat (Triticum aestivum L.) using genome-wide association study

Cited by 23 publications

References 87 publications

Mapping QTL for Phenological and Grain-Related Traits in a Mapping Population Derived from High-Zinc-Biofortified Wheat

Mapping QTL for Phenological and Grain-Related Traits in a Mapping Population Derived from High-Zinc-Biofortified Wheat

Genomic approaches for improving grain zinc and iron content in wheat

Genetic dissection of marker trait associations for grain micro-nutrients and thousand grain weight under heat and drought stress conditions in wheat

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