Molecular and phenotypic characterization of doubled haploid exotic introgression lines for nitrogen use efficiency in maize

Sanchez, Darlene L.

doi:10.31274/etd-180810-5033

Cited by 4 publications

(5 citation statements)

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“…These short RP segments interspersed within donor segments were tested for the null hypothesis that a double recombination occurred, and were either corrected or kept as original genotype, accordingly, based on P-values from the Bayes theorem (Lipka et al, unpublished). After correction, the donor genome composition was closer to the expected 25%, compared to the original marker data, and the average number of recombination events was substantially reduced [23].…”

Section: Marker Datamentioning

confidence: 90%

Genome-wide association studies of doubled haploid exotic introgression lines for root system architecture traits in maize (Zea mays L.)

et al. 2018

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Root system architecture (RSA) is becoming recognized as important for water and nutrient acquisition in plants. This study focuses on finding single nucleotide polymorphisms (SNPs) associated with seedling RSA traits from 300 doubled haploid (DH) lines derived from crosses between Germplasm Enhancement of Maize (GEM) accessions and inbred lines PHB47 and PHZ51. These DH lines were genotyped using 62,077 SNP markers, while root and shoot phenotype data were collected from 14-day old seedlings. Genome-wide association studies (GWAS) were conducted using three models to offset false positives/negatives. Multiple SNPs associated with seedling root traits were detected, some of which were within or linked to gene models that showed expression in seedling roots. Significant trait associations involving the SNP S5_152926936 on Chromosome 5 were detected in all three models, particularly the trait network area. The SNP is within the gene model GRMZM2G021110, which is expressed in roots at seedling stage. SNPs that were significantly associated with seedling root traits, and closely linked to gene models that encode proteins associated with root development were also detected. This study shows that the GEM-DH panel may be a source of allelic diversity for genes controlling seedling root development. KeywordsMaize, Zea mays L., Root system architecture, Germplasm enhancement of maize (GEM), GWAS, Doubled haploids RightsWorks produced by employees of the U.S. Government as part of their official duties are not copyrighted within the U.S. The content of this document is not copyrighted. A R T I C L E I N F O Keywords:Maize Zea mays L. Root system architecture Germplasm enhancement of maize (GEM) GWAS Doubled haploids A B S T R A C TRoot system architecture (RSA) is becoming recognized as important for water and nutrient acquisition in plants. This study focuses on finding single nucleotide polymorphisms (SNPs) associated with seedling RSA traits from 300 doubled haploid (DH) lines derived from crosses between Germplasm Enhancement of Maize (GEM) accessions and inbred lines PHB47 and PHZ51. These DH lines were genotyped using 62,077 SNP markers, while root and shoot phenotype data were collected from 14-day old seedlings. Genome-wide association studies (GWAS) were conducted using three models to offset false positives/negatives. Multiple SNPs associated with seedling root traits were detected, some of which were within or linked to gene models that showed expression in seedling roots. Significant trait associations involving the SNP S5_152926936 on Chromosome 5 were detected in all three models, particularly the trait network area. The SNP is within the gene model GRMZM2G021110, which is expressed in roots at seedling stage. SNPs that were significantly associated with seedling root traits, and closely linked to gene models that encode proteins associated with root development were also detected. This study shows that the GEM-DH panel may be a source of allelic diversity for genes controlling seedling root develo...

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Section: Marker Datamentioning

confidence: 90%

Genome-wide association studies of doubled haploid exotic introgression lines for root system architecture traits in maize (Zea mays L.)

et al. 2018

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“…Previous studies have noted that some of the BGEM‐N lines contain very little of the recurrent parent genome (Sanchez, 2017). Seven BGEM‐N DH lines shared less than 45% identity by state with PHZ51, and those individuals (BGEM‐0005‐N, BGEM‐0107‐N, BGEM‐0121‐N, BGEM‐0129‐N, BGEM‐0215‐N, BGEM‐0227‐N, and BGEM‐0248‐N) were excluded from further analysis (Figure S1).…”

Section: Methodsmentioning

confidence: 99%

Performance and phenotypic stability of maize hybrids containing exotic introgressions in multi‐environment trials

Perkins,

Lima,

Kaeppler

et al. 2024

Crop Science

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Maize (Zea mays L.) grown in the US Midwest contains only a small fraction of the genetic diversity present in the species. Maize populations from other parts of the world may contain genetic variation that could be used to improve or increase the diversity of US germplasm. This study was conducted to assess the performance and phenotypic stability of hybrids containing diverse exotic introgressions across North American environments. Doubled haploid (DH) lines were created by the Germplasm Enhancement of Maize project from backcross 1 families that used 27 open‐pollinated populations from Latin America as donor parents and PHZ51, a non‐Stiff Stalk inbred developed in Iowa, as the recurrent parent. DH lines were testcrossed with LH195, a Stiff Stalk inbred developed in Iowa, and hybrid field trials were performed at 24 environments in the United States and Canada. Experimental hybrids had variable flowering time, plant and ear height, and test weight, but none had significantly greater yield than the PHZ51 × LH195 hybrid. The slopes of linear reaction norm models were significantly lower for the experimental hybrids than the US‐adapted reference hybrids for three traits: yield, growing degree units (GDU) to anthesis, and GDU to silking. The results suggest that unfavorable alleles and phenotypic stability should be considered when exotic open‐pollinated populations are used in US maize breeding.

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“…On the other hand, to detect the effect of trans-acting lncRNAs on genes expression regulation in diverse biological processes. According to the expression correlation between lncRNAs and mRNAs (Pearson correl-ation> 0.95), 59,577 and 22,227 co-expression relationships of lncRNAs and LN-responsive genes were found in leaf and root, respectively (Table S4). GO Fig.…”

Section: Targets Analysis Of Ln-responsive Lncrnasmentioning

confidence: 99%

“…A paper roll growth method was applied for culturing maize [59]. The growth conditions and nutrient solution were the same as previously described.…”

Section: Phenotypic Measurementmentioning

confidence: 99%

Transcriptomic and genome-wide association study reveal long noncoding RNAs responding to nitrogen deficiency in maize

Zhang

Luo

et al. 2021

BMC Plant Biol

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Background Long noncoding RNAs (lncRNAs) play important roles in essential biological processes. However, our understanding of lncRNAs as competing endogenous RNAs (ceRNAs) and their responses to nitrogen stress is still limited. Results Here, we surveyed the lncRNAs and miRNAs in maize inbred line P178 leaves and roots at the seedling stage under high-nitrogen (HN) and low-nitrogen (LN) conditions using lncRNA-Seq and small RNA-Seq. A total of 894 differentially expressed lncRNAs and 38 different miRNAs were identified. Co-expression analysis found that two lncRNAs and four lncRNA-targets could competitively combine with ZmmiR159 and ZmmiR164, respectively. To dissect the genetic regulatory by which lncRNAs might enable adaptation to limited nitrogen availability, an association mapping panel containing a high-density single–nucleotide polymorphism (SNP) array (56,110 SNPs) combined with variable LN tolerant-related phenotypes obtained from hydroponics was used for a genome-wide association study (GWAS). By combining GWAS and RNA-Seq, 170 differently expressed lncRNAs within the range of significant markers were screened. Moreover, 40 consistently LN-responsive genes including those involved in glutamine biosynthesis and nitrogen acquisition in root were identified. Transient expression assays in Nicotiana benthamiana demonstrated that LNC_002923 could inhabit ZmmiR159-guided cleavage of Zm00001d015521. Conclusions These lncRNAs containing trait-associated significant SNPs could consider to be related to root development and nutrient utilization. Taken together, the results of our study can provide new insights into the potential regulatory roles of lncRNAs in response to LN stress, and give valuable information for further screening of candidates as well as the improvement of maize resistance to LN stress.

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Molecular and phenotypic characterization of doubled haploid exotic introgression lines for nitrogen use efficiency in maize

Cited by 4 publications

References 35 publications

Genome-wide association studies of doubled haploid exotic introgression lines for root system architecture traits in maize (Zea mays L.)

Genome-wide association studies of doubled haploid exotic introgression lines for root system architecture traits in maize (Zea mays L.)

Performance and phenotypic stability of maize hybrids containing exotic introgressions in multi‐environment trials

Transcriptomic and genome-wide association study reveal long noncoding RNAs responding to nitrogen deficiency in maize

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