scholarly journals Mapping quantitative trait loci and predicting candidate genes for leaf angle in maize

2020 ◽  
Author(s):  
Ning Zhang ◽  
Xueqing Huang
Keyword(s):  
Candidate Genes ◽  
Inbred Line ◽  
Plant Architecture ◽  
Crop Yields ◽  
Recombinant Inbred Lines ◽  
Chromosome 1 ◽  
Leaf Angle ◽  
Compact Leaf ◽  
Leaf Architecture ◽  
Maize Varieties

ABSTRACTLeaf angle of maize is a fundamental determinant of plant architecture and an important trait influencing photosynthetic efficiency and crop yields. To broaden our understanding of the genetic mechanisms of leaf angle formation, we constructed an F3:4 recombinant inbred lines (RIL) population derived from a cross between a model inbred line (B73) with expanded leaf architecture and an elite inbred line (Zheng58) with compact leaf architecture to map QTL for leaf angle. A sum of 8 QTL were detected on chromosome 1, 2, 3, 4 and 8. Single QTL explained 4.3 to 14.2% of the leaf angle variance. Additionally, some important QTL were confirmed through a heterogeneous inbred family(HIF) approach. Furthermore, twenty-four candidate genes for leaf angle were predicted through whole-genome resequencing and expression analysis in qLA02-01and qLA08-01 regions. These results will be helpful to elucidate the genetic mechanism of leaf angle formation in maize and benefit to clone the favorable allele for leaf angle or develop the novel maize varieties with ideal plant architecture through marker-assisted selection.

scholarly journals Mapping quantitative trait loci and predicting candidate genes for leaf angle in maize

PLoS ONE ◽  
2021 ◽  
Vol 16 (1) ◽  
pp. e0245129
Author(s):  
Ning Zhang ◽  
Xueqing Huang
Keyword(s):  
Candidate Genes ◽  
Inbred Line ◽  
Plant Architecture ◽  
Crop Yields ◽  
Recombinant Inbred Lines ◽  
Chromosome 1 ◽  
Leaf Angle ◽  
Compact Leaf ◽  
Leaf Architecture ◽  
Maize Varieties

Leaf angle of maize is a fundamental determinant of plant architecture and an important trait influencing photosynthetic efficiency and crop yields. To broaden our understanding of the genetic mechanisms of leaf angle formation, we constructed a F3:4 recombinant inbred lines (RIL) population to map QTL for leaf angle. The RIL was derived from a cross between a model inbred line (B73) with expanded leaf architecture and an elite inbred line (Zheng58) with compact leaf architecture. A sum of eight QTL were detected on chromosome 1, 2, 3, 4 and 8. Single QTL explained 4.3 to 14.2% of the leaf angle variance. Additionally, some important QTL were confirmed through a heterogeneous inbred family (HIF) approach. Furthermore, twenty-four candidate genes for leaf angle were predicted through whole-genome re-sequencing and expression analysis in qLA02-01and qLA08-01 regions. These results will be helpful to elucidate the genetic mechanism of leaf angle formation in maize and benefit to clone the favorable allele for leaf angle. Besides, this will be helpful to develop the novel maize varieties with ideal plant architecture through marker-assisted selection.

scholarly journals Genome-Wide Association Study for Plant Architecture and Bioenergy Traits in Diverse Sorghum and Sudangrass Germplasm

Agronomy ◽  
2020 ◽  
Vol 10 (10) ◽  
pp. 1602
Author(s):  
Feng Luo ◽  
Zhongyou Pei ◽  
Xiongwei Zhao ◽  
Huifen Liu ◽  
Yiwei Jiang ◽  
...  
Keyword(s):  
Association Study ◽  
Candidate Genes ◽  
Sweet Sorghum ◽  
Plant Architecture ◽  
Genome Wide Association Study ◽  
Recombinant Inbred Lines ◽  
Genome Wide Association ◽  
Phenotypic Traits ◽  
Genome Wide ◽  
A Genome

Sorghum is an important grain, forage, and bioenergy crop. The objective of this study was to identify genetic signals associated with plant architecture and bioenergy traits in sorghum and sudangrass germplasm through a genome-wide association study (GWAS). Plant height (HT), tiller number (TN), internode number (IN), stem diameter (SD), panicle length (PL), panicle weight (PW), reducing sugar (RS) content, Brix, and protein (PRO) content were assessed in 300 germplasm consisting of grain sorghum, sweet sorghum, sudangrass, sweet sorghum-sweet sorghum recombinant inbred lines (RILs) and sudangrass-sudangrass RILs grown in three different environments over two years. Large variations of phenotypic traits were observed in the population panel. The heritability of traits were all higher than 0.5, ranging from 0.52 (PRO) to 0.92 (HT) with an average of 0.76. The population exhibited three population structures (Q) and minor relative kinship (K), assessed by using 7982 single-nucleotide polymorphisms (SNPs). After controlling Q and K, GWAS identified 24 SNPs that were significantly associated with traits, including three SNPs with HT, four with TN, four with PL, three with Brix, and ten with RS. Of them, seven SNPs were novel signals that were not identified previously, including one for HT, one for TN, one for Brix, and four for RS. The putative candidate genes involved in brassinosteroid regulatory pathway, auxin biosynthesis, carbohydrate metabolism, and sugar transport were identified underlying the significant SNPs. Identification of SNP signals and related candidate genes would enrich the current genomic resource for further molecular breeding aimed at improvement of food, feed, and biofuel productions of sorghum.

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 Identification of Candidate Gene for Internode Length in Rice to Enhance Resistance to Lodging Using QTL Analysis

Plants ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 1369
Author(s):  
Dan-Dan Zhao ◽  
Ju-Hyeong Son ◽  
Muhammad Farooq ◽  
Kyung-Min Kim
Keyword(s):  
Candidate Genes ◽  
Qtl Analysis ◽  
Middle Part ◽  
Internode Length ◽  
Stem Diameter ◽  
Chromosome 1 ◽  
Doubled Haploid Population ◽  
Lodging Resistance ◽  
Cytochrome P450 Family ◽  
Uppermost Internode

Internode length and stem diameter are the primary traits affecting the lodging resistance of rice. Traits related to the length of the panicle (LP), uppermost internode (LUI), second internode (LSI), third internode (LTI), fourth internode (LFI), lowest internode (LLI) as well as stem diameter at the uppermost internode (SDUI), second internode (SDSI), third internode (SDTI), fourth internode (SDFI), and lowest internode (SDLI) in 120 Cheongcheong/Nagdong doubled haploid population were investigated using a quantitative trait locus (QTL) analysis. Thirty-four QTL regions affected LP and the length of each internode. Twenty-six QTL regions were associated with the stem diameter of each internode. RM12285-RM212 on chromosome 1 contained 10 QTLs related to the internode length, which have overlapped for over 2 years. Twenty-three candidate genes were screened using mark interval. Among the candidate genes, Os01g0803900, named OsCYPq1, which is in the Cytochrome P450 family, might be involved in gibberellins (GA) synthesis. GA is an essential plant growth regulator that affects plant height. OsCYPq1 catalyzes oxidation steps in the middle part of the GA pathway. OsCYPq1 is expected to provide valuable information to improve the marker assessment for target traits and QTL gene cloning in rice.

Identification of Novel QTLs for Spikelet Fertility, Panicle Compactness and Phytohormone Ethylene to Decipher Poor Grain Filling of Basal Spikelets in Dense Panicle Rice

2021 ◽  
Author(s):  
Sudhanshu Sekhar ◽  
Jitendra Kumar ◽  
Soumya Mohanty ◽  
Niharika Mohanty ◽  
Rudraksh Shovan Panda ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Ethylene Production ◽  
Recombinant Inbred Lines ◽  
Grain Filling ◽  
Spikelet Fertility ◽  
Rice Cultivars ◽  
Spikelet Number ◽  
Spikelet Sterility ◽  
Ubiquitin Protein Ligase ◽  
Comparative Expression Analysis

Abstract High grain number is positively correlated with grain yield in rice, but it is compromised because of poor filling of basal spikelets in dense panicle bearing numerous spikelets. The phenomenon that turns the basal spikelets of compact panicle sterile in rice is largely unknown. In order to understand the factor(s) that possibly determines such spikelet sterility in compact panicle cultivars, QTLs and candidate genes were identified for spikelet fertility percentage, panicle compactness and ethylene production that significantly influence the grain filling using recombinant inbred lines developed from a cross between indica rice cultivars, PDK Shriram (compact, high spikelet number) and Heera (lax, low spikelet number). Novel QTLs, qSFP1.1, qSFP3.1 and qSFP6.1 for spikelet fertility percentage; qIGS3.2 and qIGS4.1 for panicle compactness; and qETH1.2, qETH3.1 and qETH4.1 for ethylene production were consistently identified in both kharif seasons of 2017 and 2018. The comparative expression analysis of candidate genes like ERF3, AP2-like ethylene-responsive transcription factor, EREBP, GBSS1, E3 ubiquitin-protein ligase GW2, and LRR receptor-like serine/threonine-protein kinase ERL1 associated with identified QTLs revealed their role in poor grain filling of basal spikelets in dense panicle. These candidate genes thus could be important for improving grain filling in compact-panicle rice cultivars through biotechnological interventions.

scholarly journals Identification of Genetic Loci and Candidate Genes Related to Grain Zinc and Iron Concentration Using a Zinc-Enriched Wheat ‘Zinc-Shakti’

2021 ◽  
Vol 12 ◽  
Author(s):  
Nagenahalli Dharmegowda Rathan ◽  
Deepmala Sehgal ◽  
Karthikeyan Thiyagarajan ◽  
Ravi Singh ◽  
Anju-Mahendru Singh ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Agronomic Traits ◽  
Recombinant Inbred Lines ◽  
Iron Concentration ◽  
Small Peptides ◽  
Growing Seasons ◽  
Grain Zinc ◽  
Pleiotropic Qtl ◽  
Genomic Regions ◽  
Yield Trials

The development of nutritionally enhanced wheat (Triticum aestivum L.) with higher levels of grain iron (Fe) and zinc (Zn) offers a sustainable solution to micronutrient deficiency among resource-poor wheat consumers. One hundred and ninety recombinant inbred lines (RILs) from ‘Kachu’ × ‘Zinc-Shakti’ cross were phenotyped for grain Fe and Zn concentrations and phenological and agronomically important traits at Ciudad Obregon, Mexico in the 2017–2018, 2018–2019, and 2019–2020 growing seasons and Diversity Arrays Technology (DArT) molecular marker data were used to determine genomic regions controlling grain micronutrients and agronomic traits. We identified seven new pleiotropic quantitative trait loci (QTL) for grain Zn and Fe on chromosomes 1B, 1D, 2B, 6A, and 7D. The stable pleiotropic QTL identified have expanded the diversity of QTL that could be used in breeding for wheat biofortification. Nine RILs with the best combination of pleiotropic QTL for Zn and Fe have been identified to be used in future crossing programs and to be screened in elite yield trials before releasing as biofortified varieties. In silico analysis revealed several candidate genes underlying QTL, including those belonging to the families of the transporters and kinases known to transport small peptides and minerals (thus assisting mineral uptake) and catalyzing phosphorylation processes, respectively.

Leaf architecture of terrestrial and epiphytic ferns from an Araucaria forest in southern Brazil

Botany ◽  
2013 ◽  
Vol 91 (11) ◽  
pp. 768-773 ◽  
Author(s):  
L. Larcher ◽  
M.R.T. Boeger ◽  
P. Soffiatti ◽  
T.I. Da Silveira
Keyword(s):  
Plant Architecture ◽  
Mechanical Design ◽  
Light Interception ◽  
Leaf Position ◽  
Southern Brazil ◽  
Leaf Architecture ◽  
Leaf Form ◽  
Araucaria Forest ◽  
Maximum Light ◽  
Rigid Structure

Studies of angiosperms have associated the mechanical design of petioles with leaf form and the occurrence of simple and compound leaves. Petiole anatomy can respond differently, according to different leaf forms, to maintain plant architecture. The present study evaluated whether this premise applies to fern leaf architecture. Leaves of five ferns (Blechnum binervatum (Poir.) C.V. Morton & Lellinger, Ctenitis falciculata (Raddi) Ching, Megalastrum connexum (Kaulf.) A.R. Smith & R.C. Moran, Microgramma squamulosa (Kaulf.) de la Sota, and Serpocaulon catharinae (Langsd. & Fisch.) A.R. Sm.) from a remnant of an Araucaria Forest in southern Brazil were collected and their morphological and anatomical traits were analyzed. Results indicate that the biomechanical patterns of these terrestrial and epiphytic ferns are similar to those reported for angiosperms, except for the presence of subepidermal sclerenchyma in fern petioles. Independently of leaf form, the rigid structure of fern petioles appears to be an important adaptation to biomechanically support leaf position for maximum light interception in forest understories.

scholarly journals A Combined Linkage and GWAS Analysis Identifies QTLs Linked to Soybean Seed Protein and Oil Content

2019 ◽  
Vol 20 (23) ◽  
pp. 5915 ◽  
Author(s):  
Tengfei Zhang ◽  
Tingting Wu ◽  
Liwei Wang ◽  
Bingjun Jiang ◽  
Caixin Zhen ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Oil Content ◽  
Genome Wide Association Study ◽  
Recombinant Inbred Lines ◽  
Soybean Seed ◽  
Snp Markers ◽  
Growth Stages ◽  
Breeding Programs ◽  
Genome Wide ◽  
Excellent Source

Soybean is an excellent source of vegetable protein and edible oil. Understanding the genetic basis of protein and oil content will improve the breeding programs for soybean. Linkage analysis and genome-wide association study (GWAS) tools were combined to detect quantitative trait loci (QTL) that are associated with protein and oil content in soybean. Three hundred and eight recombinant inbred lines (RILs) containing 3454 single nucleotide polymorphism (SNP) markers and 200 soybean accessions, including 94,462 SNPs and indels, were applied to identify QTL intervals and significant SNP loci. Intervals on chromosomes 1, 15, and 20 were correlated with both traits, and QTL qPro15-1, qPro20-1, and qOil5-1 reproducibly correlated with large phenotypic variations. SNP loci on chromosome 20 that overlapped with qPro20-1 were reproducibly connected to both traits by GWAS (p < 10−4). Twenty-five candidate genes with putative roles in protein and/or oil metabolisms within two regions (qPro15-1, qPro20-1) were identified, and eight of these genes showed differential expressions in parent lines during late reproductive growth stages, consistent with a role in controlling protein and oil content. The new well-defined QTL should significantly improve molecular breeding programs, and the identified candidate genes may help elucidate the mechanisms of protein and oil biosynthesis.

Linkage mapping and genome-wide association reveal candidate genes conferring thermotolerance of seed-set in maize

2019 ◽  
Vol 70 (18) ◽  
pp. 4849-4864 ◽  
Author(s):  
Jingyang Gao ◽  
Songfeng Wang ◽  
Zijian Zhou ◽  
Shiwei Wang ◽  
Chaopei Dong ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Linkage Mapping ◽  
Genome Wide Association Study ◽  
Seed Set ◽  
Crop Yields ◽  
Expression Profiles ◽  
Snp Markers ◽  
Genome Wide Association ◽  
Genome Wide ◽  
A Genome

AbstractIt is predicted that high-temperature stress will increasingly affect crop yields worldwide as a result of climate change. In order to determine the genetic basis of thermotolerance of seed-set in maize under field conditions, we performed mapping of quantitative trait loci (QTLs) in a recombinant inbred line (RIL) population using a collection of 8329 specifically developed high-density single-nucleotide polymorphism (SNP) markers, combined with a genome-wide association study (GWAS) of 261 diverse maize lines using 259 973 SNPs. In total, four QTLs and 17 genes associated with 42 SNPs related to thermotolerance of seed-set were identified. Among them, four candidate genes were found in both linkage mapping and GWAS. Thermotolerance of seed-set was increased significantly in near-isogenic lines (NILs) that incorporated the four candidate genes in a susceptible parent background. The expression profiles of two of the four genes showed that they were induced by high temperatures in the maize tassel in a tolerant parent background. Our results indicate that thermotolerance of maize seed-set is regulated by multiple genes each of which has minor effects, with calcium signaling playing a central role. The genes identified may be exploited in breeding programs to improve seed-set and yield of maize under heat stress.

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