scholarly journals Natural variations in the P-type ATPase heavy metal transporter ZmCd1 controlling cadmium accumulation in maize grains

2021 ◽  
Author(s):  
Bin Tang ◽  
Meijie Luo ◽  
Yunxia Zhang ◽  
Huanle Guo ◽  
Jingna Li ◽  
...  
Keyword(s):  
Heavy Metal ◽  
Molecular Markers ◽  
Genome Wide Association Study ◽  
Inbred Lines ◽  
Cd Accumulation ◽  
A Genome ◽  
Maize Varieties ◽  
Natural Variations ◽  
Maize Grain ◽  
P Type

SummaryCadmium (Cd) accumulation in maize grains is detrimental to human health. Developing maize varieties with low-Cd contents via marker-assisted selection is important for ensuring the production of maize grains safe for consumption. However, the key gene controlling maize grain Cd accumulation has not been cloned. In this study, we identified two major loci for maize grain Cd accumulation (qCd1 and qCd2) on chromosome 2 during a genome-wide association study (GWAS). The qCd1 locus was analyzed by bulked segregant RNA-seq and fine mapping with a biparental segregating population of Jing724 (low-Cd line) and Mo17 (high-Cd line). The ZmCd1 candidate gene in the qCd1 locus encodes a vacuolar membrane-localized heavy metal P-type ATPase transporter, ZmHMA3, which is orthologous to the tonoplast Cd transporter OsHMA3. Genomic DNA sequence and transcript analyses suggested that a transposon in intron 1 of ZmCd1 is responsible for the abnormal amino acid sequence in Mo17. An EMS mutant analysis and an allelism test confirmed ZmCd1 influences maize grain Cd accumulation. The natural variations in ZmCd1 were used to develop four PCR-based molecular markers, which revealed five ZmCd1 haplotypes in the GWAS population. The molecular markers were also used to predict the grain Cd contents in commonly cultivated maize germplasms in China. The predicted Cd contents for 36 inbred lines and 13 hybrids were consistent with the measured Cd contents. Furthermore, several low-Cd elite inbred lines and hybrids were identified, including Jing2416, MC01, Jingnonke728, and Jingke968. Therefore, the molecular markers developed in this study are applicable for molecular breeding and developing maize varieties with low grain Cd contents.

scholarly journals Association Mapping and Transcriptome Analysis Reveal the Genetic Architecture of Maize Kernel Size

2021 ◽  
Vol 12 ◽  
Author(s):  
Juan Ma ◽  
Lifeng Wang ◽  
Yanyong Cao ◽  
Hao Wang ◽  
Huiyong Li
Keyword(s):  
Differential Expression ◽  
Genetic Architecture ◽  
Genome Wide Association Study ◽  
Differential Expression Analysis ◽  
Inbred Lines ◽  
Kernel Size ◽  
Maize Kernel ◽  
Association Panel ◽  
Kernel Length ◽  
A Genome

Kernel length, kernel width, and kernel thickness are important traits affecting grain yield and product quality. Here, the genetic architecture of the three kernel size traits was dissected in an association panel of 309 maize inbred lines using four statistical methods. Forty-two significant single nucleotide polymorphisms (SNPs; p < 1.72E-05) and 70 genes for the three traits were identified under five environments. One and eight SNPs were co-detected in two environments and by at least two methods, respectively, and they explained 5.87–9.59% of the phenotypic variation. Comparing the transcriptomes of two inbred lines with contrasting seed size, three and eight genes identified in the association panel showed significantly differential expression between the two genotypes at 15 and 39 days after pollination, respectively. Ten and 17 genes identified by a genome-wide association study were significantly differentially expressed between the two development stages in the two genotypes. Combining environment−/method-stable SNPs and differential expression analysis, ribosomal protein L7, jasmonate-regulated gene 21, serine/threonine-protein kinase RUNKEL, AP2-EREBP-transcription factor 16, and Zm00001d035222 (cell wall protein IFF6-like) were important candidate genes for maize kernel size and development.

scholarly journals Exploring the Genetic Architecture of Root-Related Traits in Mediterranean Bread Wheat Landraces by Genome-Wide Association Analysis

Agronomy ◽  
2020 ◽  
Vol 10 (5) ◽  
pp. 613 ◽  
Author(s):  
Rubén Rufo ◽  
Silvio Salvi ◽  
Conxita Royo ◽  
Jose Soriano
Keyword(s):  
Molecular Markers ◽  
Bread Wheat ◽  
Root Development ◽  
Genome Wide Association Study ◽  
Abiotic Stress Tolerance ◽  
Genome Wide Association ◽  
Mediterranean Countries ◽  
Genome Wide ◽  
A Genome ◽  
Wheat Landraces

Background: Roots are essential for drought adaptation because of their involvement in water and nutrient uptake. As the study of the root system architecture (RSA) is costly and time-consuming, it is not generally considered in breeding programs. Thus, the identification of molecular markers linked to RSA traits is of special interest to the breeding community. The reported correlation between the RSA of seedlings and adult plants simplifies its assessment. Methods: In this study, a panel of 170 bread wheat landraces from 24 Mediterranean countries was used to identify molecular markers associated with the seminal RSA and related traits: seminal root angle, total root number, root dry weight, seed weight and shoot length, and grain yield (GY). Results: A genome-wide association study identified 135 marker-trait associations explaining 6% to 15% of the phenotypic variances for root related traits and 112 for GY. Fifteen QTL hotspots were identified as the most important for controlling root trait variation and were shown to include 31 candidate genes related to RSA traits, seed size, root development, and abiotic stress tolerance (mainly drought). Co-location for root related traits and GY was found in 17 genome regions. In addition, only four out of the fifteen QTL hotspots were reported previously. Conclusions: The variability found in the Mediterranean wheat landraces is a valuable source of root traits to introgress into adapted phenotypes through marker-assisted breeding. The study reveals new loci affecting root development in wheat.

scholarly journals Loci and natural alleles for cadmium-mediated growth responses revealed by a genome wide association study and transcriptome analysis in rice

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Jianping Yu ◽  
Chaolei Liu ◽  
Hai Lin ◽  
Bin Zhang ◽  
Xiaoxia Li ◽  
...  
Keyword(s):  
Association Study ◽  
Transcriptome Analysis ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Growth Responses ◽  
Cd Stress ◽  
New Genes ◽  
Genome Wide ◽  
A Genome ◽  
Natural Variations

Abstract Background Cadmium (Cd) is a toxic heavy metal that is harmful to the environment and human health. Cd pollution threatens the cultivation of rice (Oryza sativa L.) in many countries. Improving rice performance under Cd stress could potentially improve rice productivity. Results In this study, 9 growth traits of 188 different cultivated rice accessions under normal and Cd stress conditions were found to be highly variable during the seedling stage. Based on ~3.3 million single nucleotide polymorphisms (SNPs), 119 Cd-mediated growth response (CGR) quantitative trait loci (QTL) were identified by a genome-wide association study (GWAS), 55 of which have been validated by previously reported QTL and 64 were new CGR loci. Combined with the data from the GWAS, transcriptome analysis, gene annotations from the gene ontology (GO) Slim database, and annotations and functions of homologous genes, 148 CGR candidate genes were obtained. Additionally, several reported genes have been found to play certain roles in CGRs. Seven Cd-related cloned genes were found among the CGR genes. Natural elite haplotypes/alleles in these genes that increased Cd tolerance were identified by a haplotype analysis of a diverse mini core collection. More importantly, this study was the first to uncover the natural variations of 5 GST genes that play important roles in CGRs. Conclusion The exploration of Cd-resistant rice germplasm resources and the identification of elite natural variations related to Cd-resistance will help improve the tolerance of current major rice varieties to Cd, as well as provide raw materials and new genes for breeding Cd-resistant varieties.

scholarly journals Unraveling the Role of Maize Cell Wall Hydroxycinnamates in Digestibility, Biofuel Production and Pest Resistance Using A Multi-Parent Advanced Generation Intercross (MAGIC) Approach. 

2020 ◽  
Author(s):  
Ana López-Malvar ◽  
Rosa Ana Malvar ◽  
Ana Butrón ◽  
Pedro Revilla ◽  
Xose Carlos Souto ◽  
...  
Keyword(s):  
Cell Wall ◽  
Genome Wide Association Study ◽  
Biofuel Production ◽  
Mechanical Resistance ◽  
Nucleotide Polymorphisms ◽  
Corn Borer ◽  
A Genome ◽  
Maize Varieties ◽  
Saccharification Efficiency ◽  
Total Variability

Abstract Background: Mechanical resistance due to higher hydroxycinnamate content makes maize tissues more recalcitrant to damage by insects, less digestible by ruminants, and less suitable for biofuel production. The integrated study of the maize functional genetic variability for each hydroxycinnamate component could be crucial to identify relevant genetic variants that may be incorporated into selection programs to breed maize varieties for multiple uses. A Genome Wide Association study was carried out a in a maize Multiparent-Advanced Intercross (MAGIC) Population to indentify Single Nucleotide Polymorphisms (SNPs) associated with cell wall bound hydroxycinnamates;and we checked thereafter their relationship with SNPs significantly associated with saccharification efficiency, digestibility of organic matter and corn borer damage.Results: We found 24 SNPs, corresponding to15 QTL, significantly associated with cell wall bound hydroxycinnamates. Each SNP explained between 6 and 8% of the total variability. We define new genomic regions and genes involved in polysaccharide synthesis and modifications, and the oxidative coupling associatted to cell wall hydroxycinnamates content. Conclusions: SNPs explained a small proportion of the variability for hydroxycinnamates, saccharification efficiency, digestibility or insect damage, therefore we recommend a genomic selection approach for future breeding programs of these traits. In addition, no colocalizations were found between hydroxycinnamates and final-use-related traits so breeding strategies can be focus on each particular trait with no side effects on the others.

scholarly journals High-resolution genome-wide association study pinpoints metal transporter and chelator genes involved in the genetic control of element levels in maize grain

2021 ◽  
Vol 11 (4) ◽  
Author(s):  
Di Wu ◽  
Ryokei Tanaka ◽  
Xiaowei Li ◽  
Guillaume P Ramstein ◽  
Suong Cu ◽  
...  
Keyword(s):  
Association Study ◽  
Genetic Basis ◽  
Genome Wide Association Study ◽  
Prediction Models ◽  
Genome Wide Association ◽  
Metal Transporter ◽  
Metal Chelator ◽  
Genome Wide ◽  
A Genome ◽  
Maize Grain

AbstractDespite its importance to plant function and human health, the genetics underpinning element levels in maize grain remain largely unknown. Through a genome-wide association study in the maize Ames panel of nearly 2,000 inbred lines that was imputed with ∼7.7 million SNP markers, we investigated the genetic basis of natural variation for the concentration of 11 elements in grain. Novel associations were detected for the metal transporter genes rte2 (rotten ear2) and irt1 (iron-regulated transporter1) with boron and nickel, respectively. We also further resolved loci that were previously found to be associated with one or more of five elements (copper, iron, manganese, molybdenum, and/or zinc), with two metal chelator and five metal transporter candidate causal genes identified. The nas5 (nicotianamine synthase5) gene involved in the synthesis of nicotianamine, a metal chelator, was found associated with both zinc and iron and suggests a common genetic basis controlling the accumulation of these two metals in the grain. Furthermore, moderate predictive abilities were obtained for the 11 elemental grain phenotypes with two whole-genome prediction models: Bayesian Ridge Regression (0.33–0.51) and BayesB (0.33–0.53). Of the two models, BayesB, with its greater emphasis on large-effect loci, showed ∼4–10% higher predictive abilities for nickel, molybdenum, and copper. Altogether, our findings contribute to an improved genotype-phenotype map for grain element accumulation in maize.

scholarly journals Natural variation of an EF-hand Ca2+-binding-protein coding gene confers saline-alkaline tolerance in maize

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Yibo Cao ◽  
Ming Zhang ◽  
Xiaoyan Liang ◽  
Fenrong Li ◽  
Yunlu Shi ◽  
...  
Keyword(s):  
Genome Wide Association Study ◽  
26S Proteasome ◽  
Alkaline Condition ◽  
Alkaline Stress ◽  
Translation Efficiency ◽  
Gene Target ◽  
A Genome ◽  
Alkaline Tolerance ◽  
Maize Varieties ◽  
Ef Hand

AbstractSodium (Na+) toxicity is one of the major damages imposed on crops by saline-alkaline stress. Here we show that natural maize inbred lines display substantial variations in shoot Na+ contents and saline-alkaline (NaHCO3) tolerance, and reveal that ZmNSA1 (Na+Content under Saline-Alkaline Condition) confers shoot Na+ variations under NaHCO3 condition by a genome-wide association study. Lacking of ZmNSA1 promotes shoot Na+ homeostasis by increasing root Na+ efflux. A naturally occurred 4-bp deletion decreases the translation efficiency of ZmNSA1 mRNA, thus promotes Na+ homeostasis. We further show that, under saline-alkaline condition, Ca2+ binds to the EF-hand domain of ZmNSA1 then triggers its degradation via 26S proteasome, which in turn increases the transcripts levels of PM-H+-ATPases (MHA2 and MHA4), and consequently enhances SOS1 Na+/H+ antiporter-mediated root Na+ efflux. Our studies reveal the mechanism of Ca2+-triggered saline-alkaline tolerance and provide an important gene target for breeding saline-alkaline tolerant maize varieties.

scholarly journals Difference between Pb and Cd Accumulation in 19 Elite Maize Inbred Lines and Application Prospects

2012 ◽  
Vol 2012 ◽  
pp. 1-6 ◽  
Author(s):  
Zhiming Zhang ◽  
Feng Jin ◽  
Cui Wang ◽  
Jun Luo ◽  
Haijian Lin ◽  
...  
Keyword(s):  
Heavy Metals ◽  
Heavy Metal ◽  
Inbred Lines ◽  
Seedling Stage ◽  
Soil Bioremediation ◽  
Cd Accumulation ◽  
Cross Breeding ◽  
Maize Inbred Lines ◽  
Stems And Leaves ◽  
Application Prospects

In the last two decades, the accumulation of heavy metal in crop grains has become the study hotspot. In this study, 19 representative elite maize inbred lines and 3 hybrid varieties were investigated at the seedling stage, which can accumulate Pb and Cd in the stems and leaves, respectively. The results demonstrated that significant differences are among inbred lines for accumulation of heavy metals, implying that the Cd accumulation is significant correlation between the male parents and their hybrids and some inbred lines have been selected for cross-breeding with low Pb or Cd accumulation, such as S37, 9782, and ES40; Moreover, some inbred lines could be suitable for phytoremediation species for soil bioremediation with high levels of Pb and Cd accumulation, including 178, R08, 48-2, and Mo17ht.

scholarly journals Genome-Wide Association Study of Seed Folate Content in Common Bean

2021 ◽  
Vol 12 ◽  
Author(s):  
C. Joe Martin ◽  
Davoud Torkamaneh ◽  
Muhammad Arif ◽  
Karl Peter Pauls
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Association Study ◽  
Common Bean ◽  
Genome Wide Association Study ◽  
Folate Deficiency ◽  
Genome Wide Association ◽  
Genome Wide ◽  
A Genome ◽  
Essential Components

Plant-derived folates (Vitamin B9) are essential components of the human diet. They provide one-carbon units that are required for the synthesis of nucleic acids and proteins, and folate deficiency is associated with numerous adverse health conditions. The development of high-folate cultivars of common bean (Phaseolus vulgaris L.) and other staple crops is an important tool to combat folate deficiency. A population of 96 P. vulgaris accessions, representing major North American market classes, was grown in 2 years in Ontario, Canada. The population was genotyped for 5,361 molecular markers with an Illumina Infinium platform. Total folate was extracted from mature seeds using the tri-enzyme extraction method and quantified based on a microbiological assay with Lactobacillus rhamnosus. Significant genetic diversity for folate content was observed among the population in both years of study, and folate content had a range 113–222 μg per 100 g of seeds. Quantitative trait loci (QTL) for seed folate content were identified based on a genome-wide association study (GWAS). Six QTL were identified on Chr. 4, 6, 8, and 11, with three in each year of field trials. Both QTL on Chr. 11 occurred in genomic regions that were syntenic to seed folate QTL detected in previous work with P. vulgaris, Z. mays, and O. sativa. Candidate genes were identified for these QTL that might be targets for the development of molecular markers for selecting P. vulgaris cultivars with improved seed folate content. This work reports the largest survey of genetic diversity for seed folate content in P. vulgaris and identified several genotypes, including SCN4, Bat 93, OAC Redstar, and Pompadour 1014, that would be useful for breeding beans with higher than average folate levels.

scholarly journals GWAS and WGCNA uncover hub genes controlling salt tolerance in maize (Zea mays L.) seedlings

2021 ◽  
Author(s):  
Langlang Ma ◽  
Minyan Zhang ◽  
Jie Chen ◽  
Chunyan Qing ◽  
Shijiang He ◽  
...  
Keyword(s):  
Salt Stress ◽  
Salt Tolerance ◽  
Genome Wide Association Study ◽  
Salinity Treatment ◽  
Nucleotide Polymorphisms ◽  
Maize Seedlings ◽  
Salt Tolerant ◽  
Hub Genes ◽  
A Genome ◽  
Maize Varieties

Abstract Salt stress influences maize growth and development. To decode the genetic basis and hub genes controlling salt tolerance is a meaningful exploration for cultivating salt-tolerant maize varieties. Herein, we used an association panel consisting of 305 lines to identify the genetic loci responsible for Na+- and K+-related traits in maize seedlings. Under the salt stress, seven significant single nucleotide polymorphisms were identified using a genome-wide association study, and 120 genes were obtained by scanning the linkage disequilibrium regions of these loci. According to the transcriptome data of the above 120 genes under salinity treatment, we conducted a weighted gene co-expression network analysis. Combined the gene annotations, two SNaC/SKC (shoot Na+ content/shoot K+ content)-associated genes GRMZM2G075104 and GRMZM2G333183 were finally identified as the hub genes involved in salt tolerance. Subsequently, these two genes were verified to affect salt tolerance of maize seedlings by candidate gene association analysis. Haplotypes TTGTCCG-CT and CTT were determined as favorable/salt-tolerance haplotypes for GRMZM2G075104 and GRMZM2G333183, respectively. These findings provide novel insights into genetic architectures underlying maize salt tolerance and contribute to the cultivation of salt-tolerant varieties in maize.

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