Maize Molecular Genetics and Functional Genomics

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Plant Genetics and Genomics".

Deadline for manuscript submissions: closed (5 November 2023) | Viewed by 11279

Special Issue Editor

State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
Interests: maize; genetic; breeding; disease resistance; genome; innate immunity
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Maize is one of the most important crop species worldwide, which has exceeded rice and wheat regarding both planting area and yield. Along with the rapid progress of third-generation sequencing technology in maize genome research, maize functional genomics has significantly advanced in the last decade. Moreover, the success of whole-genome sequencing of multiple maize inbred lines has promoted the cloning and functional validation of a large number of genes related to diverse traits, such as plant height, architecture, yield, quality, flavor, resistance to biotic and abiotic stresses, and many others. An increasing number of functional genes are being applied to breeding program, targeting the improvement of maize yield and quality. Therefore, exploring the function of novel loci and genes associated with economically important traits via genomics, genetics, and molecular biology approaches, which is subsequently applied to breeding elite varieties, is an important task for maize scientists.

In this Special Issue, we aim to publish high-quality research articles and reviews on all aspects of maize functional genomics, genetics, and breeding programs, including but not limited to genomic characterization, genetic dissection of various traits (growth, development, abiotic stress, maize–pathogen interactions, etc.), gene cloning, and gene function study using genome editing and overexpression. New theories and technologies related to maize genetics and breeding are also within the scope of this issue.

Prof. Dr. Xiquan Gao
Guest Editor

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Keywords

  • maize
  • functional genomics
  • molecular genetics
  • breeding technology
  • disease resistance

Published Papers (10 papers)

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Research

Jump to: Review

19 pages, 4091 KiB  
Article
Duplicated Copy Number Variant of the Maize 9-Lipoxygenase ZmLOX5 Improves 9,10-KODA-Mediated Resistance to Fall Armyworms
by Peiguo Yuan, Pei-Cheng Huang, Timothy K. Martin, Thomas M. Chappell and Michael V. Kolomiets
Genes 2024, 15(4), 401; https://doi.org/10.3390/genes15040401 - 25 Mar 2024
Viewed by 230
Abstract
Extensive genome structure variations, such as copy number variations (CNVs) and presence/absence variations, are the basis for the remarkable genetic diversity of maize; however, the effect of CNVs on maize herbivory defense remains largely underexplored. Here, we report that the naturally occurring duplication [...] Read more.
Extensive genome structure variations, such as copy number variations (CNVs) and presence/absence variations, are the basis for the remarkable genetic diversity of maize; however, the effect of CNVs on maize herbivory defense remains largely underexplored. Here, we report that the naturally occurring duplication of the maize 9-lipoxygenase gene ZmLOX5 leads to increased resistance of maize to herbivory by fall armyworms (FAWs). Previously, we showed that ZmLOX5-derived oxylipins are required for defense against chewing insect herbivores and identified several inbred lines, including Yu796, that contained duplicated CNVs of ZmLOX5, referred to as Yu796-2×LOX5. To test whether introgression of the Yu796-2×LOX5 locus into a herbivore-susceptible B73 background that contains a single ZmLOX5 gene is a feasible approach to increase resistance, we generated a series of near-isogenic lines that contained either two, one, or zero copies of the Yu796-2×LOX5 locus in the B73 background via six backcrosses (BC6). Droplet digital PCR (ddPCR) confirmed the successful introgression of the Yu796-2×LOX5 locus in B73. The resulting B73-2×LOX5 inbred line displayed increased resistance against FAW, associated with increased expression of ZmLOX5, increased wound-induced production of its primary oxylipin product, the α-ketol, 9-hydroxy-10-oxo-12(Z),15(Z)-octadecadienoic acid (9,10-KODA), and the downstream defense hormones regulated by this molecule, 12-oxo-phytodienoic acid (12-OPDA) and abscisic acid (ABA). Surprisingly, wound-induced JA-Ile production was not increased in B73-2×LOX5, resulting from the increased JA catabolism. Furthermore, B73-2×LOX5 displayed reduced water loss in response to drought stress, likely due to increased ABA and 12-OPDA content. Taken together, this study revealed that the duplicated CNV of ZmLOX5 quantitively contributes to maize antiherbivore defense and presents proof-of-concept evidence that the introgression of naturally occurring duplicated CNVs of a defensive gene into productive but susceptible crop varieties is a feasible breeding approach for enhancing plant resistance to herbivory and tolerance to abiotic stress. Full article
(This article belongs to the Special Issue Maize Molecular Genetics and Functional Genomics)
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15 pages, 6753 KiB  
Article
Characterization of Glycosyltransferase Family 1 (GT1) and Their Potential Roles in Anthocyanin Biosynthesis in Maize
by Huangai Li, Yiping Li, Xiaofang Wang, Ziwei Jiao, Wei Zhang and Yan Long
Genes 2023, 14(11), 2099; https://doi.org/10.3390/genes14112099 - 18 Nov 2023
Viewed by 960
Abstract
Glycosyltransferase family 1 (GT1) is a large group of proteins that play critical roles in secondary metabolite biosynthesis in plants. However, the GT1 family is not well studied in maize. In this study, 107 GT1 unigenes were identified in the maize reference genome [...] Read more.
Glycosyltransferase family 1 (GT1) is a large group of proteins that play critical roles in secondary metabolite biosynthesis in plants. However, the GT1 family is not well studied in maize. In this study, 107 GT1 unigenes were identified in the maize reference genome and classified into 16 groups according to their phylogenetic relationship. GT1s are unevenly distributed across all ten maize chromosomes, occurring as gene clusters in some chromosomes. Collinearity analysis revealed that gene duplication events, whole-genome or segmental duplication, and tandem duplication occurred at a similar frequency, indicating that both types of gene duplication play notable roles in the expansion of the GT1 gene family. Expression analysis showed GT1s expressing in all tissues with specific expression patterns of each GT1, suggesting that they might participate in multiple biological processes during the whole growth and development stages. Furthermore, 16 GT1s were identified to have similar expression patterns to those of anthocyanidin synthase (ANS), the critical enzyme in anthocyanin biosynthesis. Molecular docking was carried out to examine the affinity of GT1s with substrates in anthocyanin biosynthesis. This study provides valuable information on the GT1s of maize and will promote the development of research on their biological functions in the biosynthesis of other secondary metabolites. Full article
(This article belongs to the Special Issue Maize Molecular Genetics and Functional Genomics)
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19 pages, 2634 KiB  
Article
Transcriptome Analysis and QTL Mapping Identify Candidate Genes and Regulatory Mechanisms Related to Low-Temperature Germination Ability in Maize
by Lei Du, Xin Peng, Hao Zhang, Wangsen Xin, Kejun Ma, Yongzhong Liu and Guangcan Hu
Genes 2023, 14(10), 1917; https://doi.org/10.3390/genes14101917 - 08 Oct 2023
Cited by 1 | Viewed by 936
Abstract
Low-temperature germination ability (LTGA) is an important characteristic for spring sowing maize. However, few maize genes related to LTGA were confirmed, and the regulatory mechanism is less clear. Here, maize-inbred lines Ye478 and Q1 with different LTGA were used to perform transcriptome analysis [...] Read more.
Low-temperature germination ability (LTGA) is an important characteristic for spring sowing maize. However, few maize genes related to LTGA were confirmed, and the regulatory mechanism is less clear. Here, maize-inbred lines Ye478 and Q1 with different LTGA were used to perform transcriptome analysis at multiple low-temperature germination stages, and a co-expression network was constructed by weighted gene co-expression network analysis (WGCNA). Data analysis showed that 7964 up- and 5010 down-regulated differentially expressed genes (DEGs) of Ye478 were identified at low-temperature germination stages, while 6060 up- and 2653 down-regulated DEGs of Q1 were identified. Gene ontology (GO) enrichment analysis revealed that ribosome synthesis and hydrogen peroxide metabolism were enhanced and mRNA metabolism was weakened under low-temperature stress for Ye478, while hydrogen peroxide metabolism was enhanced and mRNA metabolism was weakened for Q1. DEGs pairwise comparisons between the two genotypes found that Ye478 performed more ribosome synthesis at low temperatures compared with Q1. WGCNA analysis based on 24 transcriptomes identified 16 co-expressed modules. Of these, the MEbrown module was highly correlated with Ye478 at low-temperature stages and catalase and superoxide dismutase activity, and the MEred, MEgreen, and MEblack modules were highly correlated with Ye478 across low-temperature stages, which revealed a significant association between LTGA and these modules. GO enrichment analysis showed the MEbrown and MEred modules mainly functioned in ribosome synthesis and cell cycle, respectively. In addition, we conducted quantitative trait loci (QTL) analysis based on a doubled haploid (DH) population constructed by Ye478 and Q1 and identified a major QTL explanting 20.6% of phenotype variance on chromosome 1. In this QTL interval, we found three, four, and three hub genes in the MEbrown, MEred, and MEgreen modules, of which two hub genes (Zm00001d031951, Zm00001d031953) related to glutathione metabolism and one hub gene (Zm00001d031617) related to oxidoreductase activity could be the candidate genes for LTGA. These biological functions and candidate genes will be helpful in understanding the regulatory mechanism of LTGA and the directional improvement of maize varieties for LTGA. Full article
(This article belongs to the Special Issue Maize Molecular Genetics and Functional Genomics)
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15 pages, 2126 KiB  
Article
Identification of Candidate QTLs and Genes for Ear Diameter by Multi-Parent Population in Maize
by Fuyan Jiang, Li Liu, Ziwei Li, Yaqi Bi, Xingfu Yin, Ruijia Guo, Jing Wang, Yudong Zhang, Ranjan Kumar Shaw and Xingming Fan
Genes 2023, 14(6), 1305; https://doi.org/10.3390/genes14061305 - 20 Jun 2023
Cited by 2 | Viewed by 1178
Abstract
Ear diameter (ED) is a critical component of grain yield (GY) in maize (Zea mays L.). Studying the genetic basis of ED in maize is of great significance in enhancing maize GY. Against this backdrop, this study was framed to (1) map [...] Read more.
Ear diameter (ED) is a critical component of grain yield (GY) in maize (Zea mays L.). Studying the genetic basis of ED in maize is of great significance in enhancing maize GY. Against this backdrop, this study was framed to (1) map the ED-related quantitative trait locus (QTL) and SNPs associated with ED; and (2) identify putative functional genes that may affect ED in maize. To accomplish this, an elite maize inbred line, Ye107, which belongs to the Reid heterotic group, was used as a common parent and crossed with seven elite inbred lines from three different heterotic groups (Suwan1, Reid, and nonReid) that exhibited abundant genetic variation in ED. This led to the construction of a multi-parent population consisting of 1215 F7 recombinant inbred lines (F7RILs). A genome-wide association study (GWAS) and linkage analysis were then conducted for the multi-parent population using 264,694 high-quality SNPs generated via the genotyping-by-sequencing method. Our study identified a total of 11 SNPs that were significantly associated with ED through the GWAS, and three QTLs were revealed by the linkage analysis for ED. The major QTL on chromosome 1 was co-identified in the region by the GWAS at SNP_143985532. SNP_143985532, located upstream of the Zm00001d030559 gene, encodes a callose synthase that is expressed in various tissues, with the highest expression level in the maize ear primordium. Haplotype analysis indicated that the haplotype B (allele AA) of Zm00001d030559 was positively correlated with ED. The candidate genes and SNPs identified in this study provide crucial insights for future studies on the genetic mechanism of maize ED formation, cloning of ED-related genes, and genetic improvement of ED. These results may help develop important genetic resources for enhancing maize yield through marker-assisted breeding. Full article
(This article belongs to the Special Issue Maize Molecular Genetics and Functional Genomics)
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16 pages, 1347 KiB  
Article
Evaluating the Genetic Background Effect on Dissecting the Genetic Basis of Kernel Traits in Reciprocal Maize Introgression Lines
by Ruixiang Liu, Yakun Cui, Lingjie Kong, Fei Zheng, Wenming Zhao, Qingchang Meng, Jianhua Yuan, Meijing Zhang and Yanping Chen
Genes 2023, 14(5), 1044; https://doi.org/10.3390/genes14051044 - 06 May 2023
Viewed by 1051
Abstract
Maize yield is mostly determined by its grain size. Although numerous quantitative trait loci (QTL) have been identified for kernel-related traits, the application of these QTL in breeding programs has been strongly hindered because the populations used for QTL mapping are often different [...] Read more.
Maize yield is mostly determined by its grain size. Although numerous quantitative trait loci (QTL) have been identified for kernel-related traits, the application of these QTL in breeding programs has been strongly hindered because the populations used for QTL mapping are often different from breeding populations. However, the effect of genetic background on the efficiency of QTL and the accuracy of trait genomic prediction has not been fully studied. Here, we used a set of reciprocal introgression lines (ILs) derived from 417F × 517F to evaluate how genetic background affects the detection of QTLassociated with kernel shape traits. A total of 51 QTL for kernel size were identified by chromosome segment lines (CSL) and genome-wide association studies (GWAS) methods. These were subsequently clustered into 13 common QTL based on their physical position, including 7 genetic-background-independent and 6 genetic-background-dependent QTL, respectively. Additionally, different digenic epistatic marker pairs were identified in the 417F and 517F ILs. Therefore, our results demonstrated that genetic background strongly affected not only the kernel size QTL mapping via CSL and GWAS but also the genomic prediction accuracy and epistatic detection, thereby enhancing our understanding of how genetic background affects the genetic dissection of grain size-related traits. Full article
(This article belongs to the Special Issue Maize Molecular Genetics and Functional Genomics)
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20 pages, 4771 KiB  
Article
Genome-Wide Association Study Identified Novel SNPs Associated with Chlorophyll Content in Maize
by Yueting Jin, Dan Li, Meiling Liu, Zhenhai Cui, Daqiu Sun, Cong Li, Ao Zhang, Huiying Cao and Yanye Ruan
Genes 2023, 14(5), 1010; https://doi.org/10.3390/genes14051010 - 29 Apr 2023
Cited by 2 | Viewed by 1227
Abstract
Chlorophyll is an essential component that captures light energy to drive photosynthesis. Chlorophyll content can affect photosynthetic activity and thus yield. Therefore, mining candidate genes of chlorophyll content will help increase maize production. Here, we performed a genome-wide association study (GWAS) on chlorophyll [...] Read more.
Chlorophyll is an essential component that captures light energy to drive photosynthesis. Chlorophyll content can affect photosynthetic activity and thus yield. Therefore, mining candidate genes of chlorophyll content will help increase maize production. Here, we performed a genome-wide association study (GWAS) on chlorophyll content and its dynamic changes in 378 maize inbred lines with extensive natural variation. Our phenotypic assessment showed that chlorophyll content and its dynamic changes were natural variations with a moderate genetic level of 0.66/0.67. A total of 19 single-nucleotide polymorphisms (SNPs) were found associated with 76 candidate genes, of which one SNP, 2376873-7-G, co-localized in chlorophyll content and area under the chlorophyll content curve (AUCCC). Zm00001d026568 and Zm00001d026569 were highly associated with SNP 2376873-7-G and encoded pentatricopeptide repeat-containing protein and chloroplastic palmitoyl-acyl carrier protein thioesterase, respectively. As expected, higher expression levels of these two genes are associated with higher chlorophyll contents. These results provide a certain experimental basis for discovering the candidate genes of chlorophyll content and finally provide new insights for cultivating high-yield and excellent maize suitable for planting environment. Full article
(This article belongs to the Special Issue Maize Molecular Genetics and Functional Genomics)
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13 pages, 3051 KiB  
Article
Proteome and Ubiquitylome Analyses of Maize Endoplasmic Reticulum under Heat Stress
by Chunyan Gao, Xiaohui Peng, Luoying Zhang, Qi Zhao, Liguo Ma, Qi Yu, Xuechun Lian, Lei Gao, Langyu Xiong and Shengben Li
Genes 2023, 14(3), 749; https://doi.org/10.3390/genes14030749 - 19 Mar 2023
Cited by 2 | Viewed by 1496
Abstract
High temperatures severely affect plant growth and pose a threat to global crop production. Heat causes the accumulation of misfolded proteins in the endoplasmic reticulum(ER), as well as triggering the heat-shock response (HSR) in the cytosol and the unfolded protein response (UPR) in [...] Read more.
High temperatures severely affect plant growth and pose a threat to global crop production. Heat causes the accumulation of misfolded proteins in the endoplasmic reticulum(ER), as well as triggering the heat-shock response (HSR) in the cytosol and the unfolded protein response (UPR) in the ER. Excessive misfolded proteins undergo further degradation through ER-associated degradation (ERAD). Although much research on the plant heat stress response has been conducted, the regulation of ER-localized proteins has not been well-studied thus far. We isolated the microsome fraction from heat-treated and untreated maize seedlings and performed proteome and ubiquitylome analyses. Of the 8306 total proteins detected in the proteomics analysis, 1675 proteins were significantly up-regulated and 708 proteins were significantly down-regulated. Global ubiquitination analysis revealed 1780 proteins with at least one ubiquitination site. Motif analysis revealed that alanine and glycine are the preferred amino acids upstream and downstream of ubiquitinated lysine sites. ERAD components were found to be hyper-ubiquitinated after heat treatment, implying the feedback regulation of ERAD activity through protein degradation. Full article
(This article belongs to the Special Issue Maize Molecular Genetics and Functional Genomics)
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13 pages, 2806 KiB  
Article
Coronatine-Based Gene Expression Changes Impart Partial Resistance to Fall Armyworm (Spodoptera frugiperda) in Seedling Maize
by Yuxuan Lou, Xiaoxiao Jin, Zhiguo Jia, Yuqi Sun, Yiming Xu, Zihan Liu, Shuqian Tan, Fei Yi and Liusheng Duan
Genes 2023, 14(3), 735; https://doi.org/10.3390/genes14030735 - 16 Mar 2023
Viewed by 1378
Abstract
In recent years, Spodoptera frugiperda (S. frugiperda, Smith) has invaded China, seriously threatening maize production. To explore an effective method to curb the further expansion of the harm of the S. frugiperda, this experiment used maize seedlings of the [...] Read more.
In recent years, Spodoptera frugiperda (S. frugiperda, Smith) has invaded China, seriously threatening maize production. To explore an effective method to curb the further expansion of the harm of the S. frugiperda, this experiment used maize seedlings of the Zhengdan 958 three-leaf stage (V3) of maize as the material to study the effect of coronatine (COR) on the ability of maize to resist insects (S. frugiperda) at the seedling stage. The results showed that when maize was sprayed with 0.05 μM COR, the newly incubated larvae of S. frugiperda had the least leaf feeding. It was found that 0.05 μM COR significantly increased the contents of abscisic acid (ABA) and jasmonate (JA) in maize leaves through the determination of hormone content. Moreover, transcriptome sequencing revealed that the expression of six genes (ZmBX1, ZmBX2, ZmBX3, ZmBX4, ZmBX5 and ZmBX6), which are associated with the synthesis of benzoxazinoid, were upregulated. Nine genes (ZmZIM3, ZmZIM4, ZmZIM10, ZmZIM13, ZmZIM18, ZmZIM23, ZmZIM27, ZmZIM28 and ZmZIM38) of JA-Zim Domain (JAZ) protein in the JA signal pathway, and seven genes (ZmPRH19, ZmPRH18, Zm00001d024732, Zm00001d034109, Zm00001d026269, Zm00001d028574 and Zm00001d013220) of ABA downstream response protein Group A Type 2C Protein Phosphatase (PP2C) were downregulated. These results demonstrated that COR could induce anti-insect factors and significantly improve insect resistance in seedling maize, which laid a theoretical foundation for further study of the mechanism of COR improving insect resistance in seedling maize, and provided data references for the use of COR as an environmentally friendly pest control method. Full article
(This article belongs to the Special Issue Maize Molecular Genetics and Functional Genomics)
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Review

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21 pages, 2772 KiB  
Review
Hotspot Regions of Quantitative Trait Loci and Candidate Genes for Ear-Related Traits in Maize: A Literature Review
by Xingjie Zhang, Jiachen Sun, Yudong Zhang, Jinfeng Li, Meichen Liu, Linzhuo Li, Shaoxiong Li, Tingzhao Wang, Ranjan Kumar Shaw, Fuyan Jiang and Xingming Fan
Genes 2024, 15(1), 15; https://doi.org/10.3390/genes15010015 (registering DOI) - 21 Dec 2023
Cited by 1 | Viewed by 1009
Abstract
In this study, hotspot regions, QTL clusters, and candidate genes for eight ear-related traits of maize (ear length, ear diameter, kernel row number, kernel number per row, kernel length, kernel width, kernel thickness, and 100-kernel weight) were summarized and analyzed over the past [...] Read more.
In this study, hotspot regions, QTL clusters, and candidate genes for eight ear-related traits of maize (ear length, ear diameter, kernel row number, kernel number per row, kernel length, kernel width, kernel thickness, and 100-kernel weight) were summarized and analyzed over the past three decades. This review aims to (1) comprehensively summarize and analyze previous studies on QTLs associated with these eight ear-related traits and identify hotspot bin regions located on maize chromosomes and key candidate genes associated with the ear-related traits and (2) compile major and stable QTLs and QTL clusters from various mapping populations and mapping methods and techniques providing valuable insights for fine mapping, gene cloning, and breeding for high-yield and high-quality maize. Previous research has demonstrated that QTLs for ear-related traits are distributed across all ten chromosomes in maize, and the phenotypic variation explained by a single QTL ranged from 0.40% to 36.76%. In total, 23 QTL hotspot bins for ear-related traits were identified across all ten chromosomes. The most prominent hotspot region is bin 4.08 on chromosome 4 with 15 QTLs related to eight ear-related traits. Additionally, this study identified 48 candidate genes associated with ear-related traits. Out of these, five have been cloned and validated, while twenty-eight candidate genes located in the QTL hotspots were defined by this study. This review offers a deeper understanding of the advancements in QTL mapping and the identification of key candidates associated with eight ear-related traits. These insights will undoubtedly assist maize breeders in formulating strategies to develop higher-yield maize varieties, contributing to global food security. Full article
(This article belongs to the Special Issue Maize Molecular Genetics and Functional Genomics)
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16 pages, 1435 KiB  
Review
Advancements in Research on Prevention and Control Strategies for Maize White Spot Disease
by Enyun Xing, Xingming Fan, Fuyan Jiang and Yudong Zhang
Genes 2023, 14(11), 2061; https://doi.org/10.3390/genes14112061 - 10 Nov 2023
Viewed by 973
Abstract
Maize white spot (MWS), caused by the bacterium Pantoea ananatis, is a serious disease that significantly impacts maize production and productivity. In recent years, outbreaks of white spot disease have resulted in substantial maize yield losses in southwest China. Researchers from various [...] Read more.
Maize white spot (MWS), caused by the bacterium Pantoea ananatis, is a serious disease that significantly impacts maize production and productivity. In recent years, outbreaks of white spot disease have resulted in substantial maize yield losses in southwest China. Researchers from various countries worldwide have conducted extensive research on this pathogen, including its isolation and identification, the localization of resistance genes, transmission pathways, as well as potential control measures. However, the information related to this disease remains fragmented, and standardized preventive and control strategies have not yet been established. In light of this, this review aims to comprehensively summarize the research findings on MWS, providing valuable insights into understanding its occurrence, prevention, and control measures in the southwestern and southern regions of China while also mitigating the detrimental impact and losses caused by MWS on maize production in China and across the world. Full article
(This article belongs to the Special Issue Maize Molecular Genetics and Functional Genomics)
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