scholarly journals Genome-Wide Association Study Using a Multiparent Advanced Generation Intercross (MAGIC) Population Identified QTLs and Candidate Genes to Predict Shoot and Grain Zinc Contents in Rice

Agriculture ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 70
Author(s):  
Shilei Liu ◽  
Wenli Zou ◽  
Xiang Lu ◽  
Jianmin Bian ◽  
Haohua He ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Phenotypic Variation ◽  
Gene Annotation ◽  
Indica Rice ◽  
Snp Array ◽  
Seedling Stage ◽  
Mature Stage ◽  
Parental Lines ◽  
Advanced Generation ◽  
Magic Population

Zinc (Zn) is an essential trace element for the growth and development of both humans and plants. Increasing the accumulation of Zn in rice grains is important for the world’s nutrition and health. In this study, we used a multiparent advanced generation intercross (MAGIC) population constructed using four parental lines and genotyped using a 55 K rice SNP array to identify QTLs related to Zn2+ concentrations in shoots at the seedling stage and grains at the mature stage. Five QTLs were detected as being associated with shoot Zn2+ concentration at the seedling stage, which explained 3.7–5.7% of the phenotypic variation. Six QTLs were detected as associated with grain Zn2+ concentration at the mature stage, which explained 5.5–8.9% of the phenotypic variation. Among the QTLs, qSZn2-1/qGZn2 and qSZn3/qGZn3 were identified as being associated with both the shoot and grain contents. Based on gene annotation and literature information, 16 candidate genes were chosen in the regions of qSZn1, qSZn2-1/qGZn2, qSZn3/qGZn3, qGZn7, and qGZn8. Analysis of candidate genes through qRT-PCR, complementation assay using the yeast Zn-uptake-deficient double-mutant ZHY3, and sequencing of the four parental lines suggested that LOC_Os02g06010 may play an important role in Zn2+ accumulation in indica rice.

QTL identification for salt tolerance related traits at the seedling stage in indica rice using a multi-parent advanced generation intercross (MAGIC) population

2020 ◽  
Vol 92 (2) ◽  
pp. 365-373 ◽  
Author(s):  
Ya Zhang ◽  
Kimberly S. Ponce ◽  
Lijun Meng ◽  
Panchali Chakraborty ◽  
Qingyuan Zhao ◽  
...  
Keyword(s):  
Salt Tolerance ◽  
Indica Rice ◽  
Seedling Stage ◽  
Qtl Identification ◽  
Advanced Generation ◽  
Magic Population

scholarly journals Identification of a Novel QTL for Chlorate Resistance in Rice (Oryza sativa L.)

Agriculture ◽  
2020 ◽  
Vol 10 (8) ◽  
pp. 360 ◽  
Author(s):  
Nkulu Rolly Kabange ◽  
So-Yeon Park ◽  
Dongjin Shin ◽  
So-Myeong Lee ◽  
Su-Min Jo ◽  
...  
Keyword(s):  
Oryza Sativa ◽  
Candidate Genes ◽  
Phenotypic Variation ◽  
Oryza Sativa L ◽  
In Silico Analysis ◽  
Parental Line ◽  
Chlorate Resistance ◽  
Specific Pcr ◽  
Significant Difference ◽  
Parental Lines

Chlorate resistance analysis is an effective approach commonly used to distinguish the genetic variation between Oryza sativa L. ssp. indica and japonica, and predict the nitrogen use efficiency (NUE). This study aimed at investigating the response of a doubled haploid (DH) population derived from anther culture of 93-11 × Milyang352 exposed to 0.1% potassium chlorate (KClO3) at the seedling stage. The results revealed that the parental rice lines 93-11 (indica) and Milyang352 (japonica) showed distinctive phenotypic responses. The parental line 93-11 scored highly sensitive (0% survival) and Milyang352 scored resistant (66.7% survival) 7 days after treatment. The DH lines reflected the differential phenotypic response observed in parental lines. Interestingly, we identified a novel quantitative trait locus (QTL) for chlorate resistance on chromosome 3 (qCHR-3, 136 cM, logarithm of the odds—LOD: 4.1) using Kompetitive Allele-Specific PCR (KASP) markers. The additive effect (−11.97) and phenotypic variation explained (PVE; 14.9%) indicated that the allele from Milyang352 explained the observed phenotypic variation. In addition, shoot growth showed a significant difference between parental lines, but not root growth. Moreover, in silico analysis identified candidate genes with diverse and interesting molecular and physiological functions. Therefore, this study suggested that the QTL qCHR-3 harbors promising candidate genes that could play a role in the regulation of nitrogen metabolism in rice.

scholarly journals Genetic Mapping by Integration of 55K SNP Array and KASP Markers Reveals Candidate Genes for Important Agronomic Traits in Hexaploid Wheat

2021 ◽  
Vol 12 ◽  
Author(s):  
Hongchun Xiong ◽  
Yuting Li ◽  
Huijun Guo ◽  
Yongdun Xie ◽  
Linshu Zhao ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Phenotypic Variation ◽  
Agronomic Traits ◽  
Recombinant Inbred Lines ◽  
Wheat Yield ◽  
Snp Array ◽  
Heading Date ◽  
Sequencing Data ◽  
Gene Encoding ◽  
Kasp Markers

Agronomic traits such as heading date (HD), plant height (PH), thousand grain weight (TGW), and spike length (SL) are important factors affecting wheat yield. In this study, we constructed a high-density genetic linkage map using the Wheat55K SNP Array to map quantitative trait loci (QTLs) for these traits in 207 recombinant inbred lines (RILs). A total of 37 QTLs were identified, including 9 QTLs for HD, 7 QTLs for PH, 12 QTLs for TGW, and 9 QTLs for SL, which explained 3.0–48.8% of the phenotypic variation. Kompetitive Allele Specific PCR (KASP) markers were developed based on sequencing data and used for validation of the stably detected QTLs on chromosomes 3A, 4B and 6A using 400 RILs. A QTL cluster on chromosome 4B for PH and TGW was delimited to a 0.8 Mb physical interval explaining 12.2–22.8% of the phenotypic variation. Gene annotations and analyses of SNP effects suggested that a gene encoding protein Photosynthesis Affected Mutant 68, which is essential for photosystem II assembly, is a candidate gene affecting PH and TGW. In addition, the QTL for HD on chromosome 3A was narrowed down to a 2.5 Mb interval, and a gene encoding an R3H domain-containing protein was speculated to be the causal gene influencing HD. The linked KASP markers developed in this study will be useful for marker-assisted selection in wheat breeding, and the candidate genes provide new insight into genetic study for those traits in wheat.

scholarly journals QTL Analysis of Five Morpho-Physiological Traits in Bread Wheat Using Two Mapping Populations Derived from Common Parents

Genes ◽  
2021 ◽  
Vol 12 (4) ◽  
pp. 604
Author(s):  
Paolo Vitale ◽  
Fabio Fania ◽  
Salvatore Esposito ◽  
Ivano Pecorella ◽  
Nicola Pecchioni ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Recombinant Inbred Lines ◽  
Snp Array ◽  
Heading Date ◽  
Tiller Number ◽  
Genetic Maps ◽  
Yield Potential ◽  
Adaptation To Climate Change ◽  
Map Resolution ◽  
Mapping Populations

Traits such as plant height (PH), juvenile growth habit (GH), heading date (HD), and tiller number are important for both increasing yield potential and improving crop adaptation to climate change. In the present study, these traits were investigated by using the same bi-parental population at early (F2 and F2-derived F3 families) and late (F6 and F7, recombinant inbred lines, RILs) generations to detect quantitative trait loci (QTLs) and search for candidate genes. A total of 176 and 178 lines were genotyped by the wheat Illumina 25K Infinium SNP array. The two genetic maps spanned 2486.97 cM and 3732.84 cM in length, for the F2 and RILs, respectively. QTLs explaining the highest phenotypic variation were found on chromosomes 2B, 2D, 5A, and 7D for HD and GH, whereas those for PH were found on chromosomes 4B and 4D. Several QTL detected in the early generations (i.e., PH and tiller number) were not detected in the late generations as they were due to dominance effects. Some of the identified QTLs co-mapped to well-known adaptive genes (i.e., Ppd-1, Vrn-1, and Rht-1). Other putative candidate genes were identified for each trait, of which PINE1 and PIF4 may be considered new for GH and TTN in wheat. The use of a large F2 mapping population combined with NGS-based genotyping techniques could improve map resolution and allow closer QTL tagging.

scholarly journals Genome-Wide Association Study Reveals the Genetic Basis of Cold Tolerance in Rice at the Seedling Stage

Agriculture ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 318
Author(s):  
Tae-Ho Ham ◽  
Yebin Kwon ◽  
Yoonjung Lee ◽  
Jisu Choi ◽  
Joohyun Lee
Keyword(s):  
Association Study ◽  
Candidate Genes ◽  
Cold Tolerance ◽  
Genome Wide Association Study ◽  
Seedling Stage ◽  
Genome Wide Association ◽  
Matrix Analysis ◽  
Rice Seedlings ◽  
Genome Wide ◽  
A Genome

We conducted a genome-wide association study (GWAS) of cold tolerance in a collection of 127 rice accessions, including 57 Korean landraces at the seedling stage. Cold tolerance of rice seedlings was evaluated in a growth chamber under controlled conditions and scored on a 0–9 scale, based on their low-temperature response and subsequent recovery. GWAS, together with principal component analysis (PCA) and kinship matrix analysis, revealed four quantitative trait loci (QTLs) on chromosomes 1, 4, and 5 that explained 16.5% to 18.5% of the variance in cold tolerance. The genomic region underlying the QTL on chromosome four overlapped with a previously reported QTL associated with cold tolerance in rice seedlings. Similarly, one of the QTLs identified on chromosome five overlapped with a previously reported QTL associated with seedling vigor. Subsequent bioinformatic and haplotype analyses revealed three candidate genes affecting cold tolerance within the linkage disequilibrium (LD) block of these QTLs: Os01g0357800, encoding a pentatricopeptide repeat (PPR) domain-containing protein; Os05g0171300, encoding a plastidial ADP-glucose transporter; and Os05g0400200, encoding a retrotransposon protein, Ty1-copia subclass. The detected QTLs and further evaluation of these candidate genes in the future will provide strategies for developing cold-tolerant rice in breeding programs.

scholarly journals Genome-wide analysis of changes in miRNA and target gene expression reveals key roles in heterosis for Chinese cabbage biomass

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Peirong Li ◽  
Tongbing Su ◽  
Deshuang Zhang ◽  
Weihong Wang ◽  
Xiaoyun Xin ◽  
...  
Keyword(s):  
Chinese Cabbage ◽  
Leaf Development ◽  
Target Genes ◽  
Expression Patterns ◽  
Seedling Stage ◽  
Differentially Expressed ◽  
Small Rna Sequencing ◽  
Leaf Morphogenesis ◽  
Expression Levels ◽  
Parental Lines

AbstractHeterosis is a complex phenomenon in which hybrids show better phenotypic characteristics than their parents do. Chinese cabbage (Brassica rapa L. spp. pekinensis) is a popular leafy crop species, hybrids of which are widely used in commercial production; however, the molecular basis of heterosis for biomass of Chinese cabbage is poorly understood. We characterized heterosis in a Chinese cabbage F1 hybrid cultivar and its parental lines from the seedling stage to the heading stage; marked heterosis of leaf weight and biomass yield were observed. Small RNA sequencing revealed 63 and 50 differentially expressed microRNAs (DEMs) at the seedling and early-heading stages, respectively. The expression levels of the majority of miRNA clusters in the F1 hybrid were lower than the mid-parent values (MPVs). Using degradome sequencing, we identified 1,819 miRNA target genes. Gene ontology (GO) analyses demonstrated that the target genes of the MPV-DEMs and low parental expression level dominance (ELD) miRNAs were significantly enriched in leaf morphogenesis, leaf development, and leaf shaping. Transcriptome analysis revealed that the expression levels of photosynthesis and chlorophyll synthesis-related MPV-DEGs (differentially expressed genes) were significantly different in the F1 hybrid compared to the parental lines, resulting in increased photosynthesis capacity and chlorophyll content in the former. Furthermore, expression of genes known to regulate leaf development was also observed at the seedling stage. Arabidopsis plants overexpressing BrGRF4.2 and bra-miR396 presented increased and decreased leaf sizes, respectively. These results provide new insight into the regulation of target genes and miRNA expression patterns in leaf size and heterosis for biomass of B. rapa.

scholarly journals QTL mapping of root traits in wheat under different phosphorus levels using hydroponic culture

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Mengjiao Yang ◽  
Cairong Wang ◽  
Muhammad Adeel Hassan ◽  
Faji Li ◽  
Xianchun Xia ◽  
...  
Keyword(s):  
Root System ◽  
Phenotypic Diversity ◽  
Nutrient Use Efficiency ◽  
Snp Array ◽  
P Uptake ◽  
Hydroponic Culture ◽  
Seedling Stage ◽  
Root Surface Area ◽  
Root Tips ◽  
Phenotypic Effect

Abstract Background Phosphorus (P) is an important in ensuring plant morphogenesis and grain quality, therefore an efficient root system is crucial for P-uptake. Identification of useful loci for root morphological and P uptake related traits at seedling stage is important for wheat breeding. The aims of this study were to evaluate phenotypic diversity of Yangmai 16/Zhongmai 895 derived doubled haploid (DH) population for root system architecture (RSA) and biomass related traits (BRT) in different P treatments at seedling stage using hydroponic culture, and to identify QTL using 660 K SNP array based high-density genetic map. Results All traits showed significant variations among the DH lines with high heritabilities (0.76 to 0.91) and high correlations (r = 0.59 to 0.98) among all traits. Inclusive composite interval mapping (ICIM) identified 34 QTL with 4.64–20.41% of the phenotypic variances individually, and the log of odds (LOD) values ranging from 2.59 to 10.43. Seven QTL clusters (C1 to C7) were mapped on chromosomes 3DL, 4BS, 4DS, 6BL, 7AS, 7AL and 7BL, cluster C5 on chromosome 7AS (AX-109955164 - AX-109445593) with pleiotropic effect played key role in modulating root length (RL), root tips number (RTN) and root surface area (ROSA) under low P condition, with the favorable allele from Zhongmai 895. Conclusions This study carried out an imaging pipeline-based rapid phenotyping of RSA and BRT traits in hydroponic culture. It is an efficient approach for screening of large populations under different nutrient conditions. Four QTL on chromosomes 6BL (2) and 7AL (2) identified in low P treatment showed positive additive effects contributed by Zhongmai 895, indicating that Zhongmai 895 could be used as parent for P-deficient breeding. The most stable QTL QRRS.caas-4DS for ratio of root to shoot dry weight (RRS) harbored the stable genetic region with high phenotypic effect, and QTL clusters on 7A might be used for speedy selection of genotypes for P-uptake. SNPs closely linked to QTLs and clusters could be used to improve nutrient-use efficiency.

scholarly journals PSVII-37 Late-Breaking Abstract: CNV analysis of indigenous sheep reveals genes linked to disease resistance and adaptation

2020 ◽  
Vol 98 (Supplement_4) ◽  
pp. 339-339
Author(s):  
Annelin Molotsi
Keyword(s):  
Candidate Genes ◽  
Copy Number ◽  
Structural Changes ◽  
Gene Annotation ◽  
Smallholder Farmers ◽  
Copy Number Variations ◽  
Ovis Aries ◽  
Matrix Composition ◽  
Low Input ◽  
Gene Group

Abstract Smallholder farmers often make use of low-input systems, suggesting that robust and adaptable individuals are needed in these systems that have good production and reproduction in these low-input systems. One of the reasons certain individuals may be more adaptable or have higher production outputs could be due to the presence of advantageous mutations or genetic structural variants. Genetic variants, namely copy number variations (CNVs), are structural changes to the DNA and are larger than a single nucleotide. In this study, 47 sheep were investigated for the presence of CNVs. A total of 206 CNVs passed quality control. These CNVs were compared to the NCBI RefSeq Ovis aries: Oar_v4.0 to identify candidate genes located within or overlapping the copy number variations identified. Gene annotation analysis was carried out on the identified candidate genes. Gene annotation assigned the candidate genes to two gene groups. The first gene group were protein coding genes responsible for interferons that are the natural defences individuals have against viral and bacterial infection. The second gene group was found to be responsible for a variety of biological functions including transport, metabolic precursors, neurogenesis, signalling as well as bone and cartilage matrix composition along with a number of other important functions. This indicates that CNVs could have various effects on important biological process which could possibly influence an individual’s survival or even production and reproduction. This highlights the need for CNV studies to determine the influence of these CNVs and how they can be utilised in breeding programmes to improve adaptation and production outputs.

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