Research

13 pages, 782 KiB

Open AccessArticle

Identification, Interaction, Expression, and Function of QTLs on Leaf Numbers with Single-Segment Substitution Lines in Rice

by Suhong Bu, Penglin Zhan, Lilong Huang, Jichun Tang, Leyi Chen, Haitao Zhu, Zupei Liu, Lijun Meng, Guifu Liu and Shaokui Wang

Agronomy 2022, 12(12), 2968; https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy12122968 - 25 Nov 2022

Cited by 2 | Viewed by 976

Abstract

Rice leaf is a solar panel of photosynthesis and determines the light energy utilization and yield of plants. Leaf numbers appear as S-type or parabola-type growth curves throughout their development. However, the ways in which the genes regulate the process of leaf [...] Read more.

Rice leaf is a solar panel of photosynthesis and determines the light energy utilization and yield of plants. Leaf numbers appear as S-type or parabola-type growth curves throughout their development. However, the ways in which the genes regulate the process of leaf numbers still remain poorly understood. This paper first identified five QTLs associated with leaf numbers using single-segment substitution lines (SSSLs). Then, the epistatic effects between double QTLs were estimated via the decomposition of the QTL polymerization effects. Additionally, further the expression patterns and functions for these five QTLs and their epistasis were revealed by the methodologies of conditional QTL mapping and functional QTL mapping, respectively. The five SSSLs were detected as having significant additive and/or dominant effects at one or more stages, all of which increased the leaf numbers, except for the negative additive effect of the first SSSL. Seven pairs of QTLs interacted each other via three or four epistatic components, with the opposite effects in the case of single genes, i.e., most epistatic effects were negative. The five QTLs expressed their effects mainly in three stages, namely within 14 days, from 28 days to 42 days, and from 49 days to 63 days after transplantation. Positive effects and negative interactions of the QTLs were observed in the early and the late stages, but opposite interactions were observed in the middle stage. Mainly, three functional parameters, including the inflexion point, the peak value, and the degradation rate, were regulated via the QTL effects and their opposite interactions. This paper uncovered the genetic rule of five QTLs on the leaf numbers, including the interaction, expression, and function features. The information will be helpful to understand the genetic mechanism for developmental traits. Full article

(This article belongs to the Special Issue Genetics Research and Molecular Breeding of Crops)

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22 pages, 2908 KiB

Open AccessArticle

Diversity of Polish Oat Cultivars with a Glance at Breeding History and Perspectives

by Aneta Koroluk, Edyta Paczos-Grzęda, Sylwia Sowa, Maja Boczkowska and Joanna Toporowska

Agronomy 2022, 12(10), 2423; https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy12102423 - 06 Oct 2022

Cited by 3 | Viewed by 1480

Abstract

During 120 years of Polish breeding of oats (Avena sativa L.), dozens of new varieties have been developed. This study was undertaken to investigate the diversity and population structure of 72 Polish oat cultivars released since 1893. The analysis was based on [...] Read more.

During 120 years of Polish breeding of oats (Avena sativa L.), dozens of new varieties have been developed. This study was undertaken to investigate the diversity and population structure of 72 Polish oat cultivars released since 1893. The analysis was based on pedigree data as well as ISSR and REMAP marker polymorphisms. The ancestry of common oat cultivars was traced back to 124 cultivars, breeding lines, and landraces. The five most common progenitors were ‘Markische Landsorte’, ‘selection from Ligowo oat’, ‘Fransk Svarthavre’, ‘Blanche de Siberie’, and ‘selection from Schleswig-Holstein landrace’. We found that at least one of them was present in 78% of analysed objects. The studied cultivars were assigned to four groups according to the period of their breeding (before 1945, 1945–1969, 1970–2000, and after 2000) and six groups according to the breeding company (Strzelce Plant Breeding Company, DANKO Plant Breeding, Station of Plant Breeding in Rogaczewo, Małopolska Plant Breeding Company, Station of Plant Breeding in Borów, and other). A decrease in observed heterozygosity within the groups was observed only in the postwar period (1945–1969). As a result of breeders’ efforts and extensive crosses with foreign materials initiated in 1970 and 1980, new alleles were provided to the oat gene pool. The highest number of new varieties came from the Strzelce and DANKO breeding companies. There were no significant differences between modern cultivars derived from different breeding companies. However, very early breeding centres functioning before 1945 had significantly different materials from the modern ones. The population genetic structure of the studied group of cultivars appeared to be quite simple. It was shown that their genetic makeup consisted of two or three distinct gene pools, depending on the method of polymorphism assessment. The performed research proved that Polish oat breeding using traditional breeding methods—such as selection or intraspecific and interspecific crosses—although focused on improving yield and tolerance to biotic and abiotic stress, did not significantly narrow the oat gene pool and has been releasing cultivars that are competitive in the European market. Full article

(This article belongs to the Special Issue Genetics Research and Molecular Breeding of Crops)

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12 pages, 8891 KiB

Open AccessArticle

Mechanism of Early Flowering in a Landrace Naked Barley eam8.l Mutant

by Chengzhi Mao, Jinqing Xu, Handong Wang, Tongrui Chen, Haiyan Bian, En You, Yuhu Shen and Lei Wang

Agronomy 2022, 12(9), 2137; https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy12092137 - 08 Sep 2022

Cited by 1 | Viewed by 1058

Abstract

The EARLY MATURITY 8 (EAM8) gene of barley is homologous to the EARLY FLOWERING 3 (ELF3) gene in Arabidopsis, as loss-of-function mutations in this circadian clock gene promote rapid flowering. A previous study demonstrated that the early flowering phenotype [...] Read more.

The EARLY MATURITY 8 (EAM8) gene of barley is homologous to the EARLY FLOWERING 3 (ELF3) gene in Arabidopsis, as loss-of-function mutations in this circadian clock gene promote rapid flowering. A previous study demonstrated that the early flowering phenotype of a hulless barley, Lalu, was due to allele eam8.l carrying an alternative splicing mutation in intron 3 that led to intron retention. In the present study, we verified that eam8.l encoded a truncated protein. Although EAM8 was expressed at a higher level in Lalu than in other barley lines with a longer growth period, it did not negatively regulate flowering time. This result further proved that the eam8.l protein was nonfunctional in regulating flowering in barley. The early flowering phenotype of Lalu plants was strongly dependent on the biosynthesis of gibberellin (GA). The eam8.l mutation stopped the suppression of GA biosynthesis, and Lalu accumulated excessive GA, especially in leaves. This was achieved through the upregulated expression of genes in the GA pathway, including GA20ox2, LFY1, SOC1, PAP2, and FPF3. The mutation of the EAM8 gene also abolished the inhibition of FLOWERING LOCUS T-like (FT1) gene expression at night. During the night, expression levels of the FT1 gene were higher than those during the day in Lalu. However, the GA-dependent pathway and FT1 gene mechanism are two independent pathways that promote flowering in Lalu. Alleles of EAM8, therefore, demonstrated an important breeding value in barley, which is probably effective in many other day-length-sensitive crop plants as well; thus, they could be used to tune adaptation in different geographic regions and climatic conditions, a critical issue in times of global warming. Full article

(This article belongs to the Special Issue Genetics Research and Molecular Breeding of Crops)

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13 pages, 2367 KiB

Open AccessArticle

Prediction of Maize Seed Vigor Based on First-Order Difference Characteristics of Hyperspectral Data

by Huawei Cui, Yang Bing, Xiaodi Zhang, Zilin Wang, Longwei Li and Aimin Miao

Agronomy 2022, 12(8), 1899; https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy12081899 - 12 Aug 2022

Cited by 5 | Viewed by 1349

Abstract

The identification of seed vigor is of great significance to improve the seed germination rate, increase crop yield, and ensure product quality. In this study, based on a hyperspectral data acquisition system and an improved feature extraction algorithm, an identification model of the [...] Read more.

The identification of seed vigor is of great significance to improve the seed germination rate, increase crop yield, and ensure product quality. In this study, based on a hyperspectral data acquisition system and an improved feature extraction algorithm, an identification model of the germination characteristics for corn seeds was constructed. In this research, hyperspectral data acquisition and the standard corn seed germination test for Zhengdan 958 were carried out. By integrating the hyperspectral data in the spectral range of 386.7–1016.7 nm and the first derivative information of the spectral data, the root length prediction for corn seeds was successfully completed. The data regression model and prediction relationship between the spectral characteristics and seedling root length were established by principal component regression, partial least squares, and support vector regression. The first derivative information of the hyperspectral data was obtained by comparing the prediction model results with the original spectral data, which was preprocessed by Savitzky–Golay smoothing, multiplicative scatter correction, standard normal variate, and curve fitting. The results showed that the prediction model based on the first-order differential spectral data showed better performance than the one based on the spectral data obtained by other processing algorithms. By comparing the prediction results using different data characteristics and regression models, it was found that the hyperspectral method can effectively predict the root length of the seed, with the coefficient of determination reaching 0.8319. Full article

(This article belongs to the Special Issue Genetics Research and Molecular Breeding of Crops)

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9 pages, 3352 KiB

Open AccessCommunication

Biomarker Discovery for Detecting the Seed Ageing Degree and Priming Effect of Tobacco

by Yongzhi Niu, Yunye Zheng, Dongjie Zhou, Jia Zhao, Chengjing Wang, Zhoufei Wang and Limeng Zhang

Agronomy 2022, 12(8), 1897; https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy12081897 - 12 Aug 2022

Viewed by 1333

Abstract

Seed ageing is an important issue for the long-time seed storage of tobacco. Seed priming has been popularly applied in tobacco production. In this study, the development of molecular marker genes encoding proteins L-isoaspartyl methyltransferase NtPIMT1 and 8-oxoG DNA glycosylase 1 NtOGG1 to [...] Read more.

Seed ageing is an important issue for the long-time seed storage of tobacco. Seed priming has been popularly applied in tobacco production. In this study, the development of molecular marker genes encoding proteins L-isoaspartyl methyltransferase NtPIMT1 and 8-oxoG DNA glycosylase 1 NtOGG1 to detect the degree of seed ageing and the effect of seed priming is conducted in tobacco. Quantitative real-time PCR (qRT-PCR) analysis reveals that relatively higher mRNAs of NtPIMT1 and NtOGG1 are observed in the dry and early germinating seeds. The expressions of NtPIMT1 and NtOGG1 are negatively correlated with the degree of seed damage in non-pelleted and pelleted seeds after accelerated ageing treatments. The early best effects of gibberellin (GA₃) priming on speed and uniform germination are observed in 33 h primed seeds, and relatively lower expressions of NtPIMT1 and NtOGG1 are observed in priming seeds. NtPIMT1 and NtOGG1 genes have potential for use as molecular markers in detecting the seed ageing degree and priming effect of tobacco. Full article

(This article belongs to the Special Issue Genetics Research and Molecular Breeding of Crops)

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14 pages, 2836 KiB

Open AccessArticle

Unraveling the Genetic Architecture for Low Temperature Germinability-Related Traits in Rice Using Genome-Wide Association Study

by Caijing Li, Baoli Zou, Changsheng Lu, Guiting Song, Qiang Gao, Peng Wang, Guangliang Wu, Wei Jin, Hui Yin, Qin Cheng, Yanning Wang, Qi Zhong, Shiying Huang, Mengmeng Yang, Tao Huang, Haohua He and Jianmin Bian

Agronomy 2022, 12(5), 1194; https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy12051194 - 16 May 2022

Viewed by 1549

Abstract

Rice is frequently affected by cold weather at high altitudes in temperate and subtropical regions. With the popularity of direct seeding, a better understanding of the genetic mechanisms regulating cold tolerance will enable breeders to develop varieties with strong low temperature germinability (LTG). [...] Read more.

Rice is frequently affected by cold weather at high altitudes in temperate and subtropical regions. With the popularity of direct seeding, a better understanding of the genetic mechanisms regulating cold tolerance will enable breeders to develop varieties with strong low temperature germinability (LTG). In this study, six indices including low temperature germination percentage (LTGP), relative germination percentage (RGP), relative plumule length (RPL), plumule length after 6-day recovery (PLR), plumule length recovery rate (PLRR) and recovery ability of plumule length after cold stress (RAPL) were measured to assess LTG, and carried out a genome-wide association study (GWAS) to identify QTL and candidate genes related to LTG by using a natural population comprising 211 rice accessions. A total of 18 QTL including two for LTGP, three for RGP, five for PLR, four for PLRR, two for RPL and two for RAPL were uncovered on 12 chromosome regions located in chromosome 1, 2, 4, 5, 6, 9, 10 and 12. On chromosome 2, qLTGP2 and qRGP2 were co-localized at 3.3 Mb, and qPLR2 and qPLRR2 were co-localized at 5.5 Mb; qLTGP5, qPLR5 and qPLR5 were co-localized at 27.8 Mb on chromosome 5; qPLR6 and qPLRR6 were co-localized at 5.7 Mb on chromosome 6; and qPLR12 and qPLRR12 were co-localized at 23.5 Mb on chromosome 12. These results indicated that some LTG-related traits may share the same genetic pathway. For the 18 LTG-related QTL, seven QTL (qLTGP2, qRGP2, qPLR2, qPLRR2, qLTGP5, qPLR5 and qPLR5) were reported for the first time. According to candidate gene analysis, fourteen genes from five QTL (qLTGP2, qPLR2, qLTGP5, qRAPL10 and qPLR12) were considered as candidate genes and will be further functionally validated in subsequent experiments. QTL with superior candidate genes identified in this study will be useful in improving cold tolerance in rice cultivars. The rice varieties with strong LTG identified in this study will enrich the resources of rice cultivation project. Full article

(This article belongs to the Special Issue Genetics Research and Molecular Breeding of Crops)

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16 pages, 13086 KiB

Open AccessArticle

Mapping of Quantitative Trait Loci Underlying Nodule Traits in Soybean (Glycine max (L.) Merr.) and Identification of Genes Whose Expression Is Affected by the Sinorhizobium fredii HH103 Effector Proteins NopL and NopT

by Hejia Ni, Yang Peng, Jinhui Wang, Jing Wang, Yantong Yuan, Tingting Fu, Zikun Zhu, Jialin Zhang, Xipeng Pan, Zhuoling Cui, Chunyan Liu, Qingshan Chen and Dawei Xin

Agronomy 2022, 12(4), 946; https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy12040946 - 15 Apr 2022

Cited by 7 | Viewed by 1877

Abstract

Symbiotic nitrogen fixation provides most of the nitrogen required for soybean growth. Rhizobial nodulation outer proteins (Nops) have been reported to influence host specificity during symbiosis establishment. However, the host proteins that interact with Nops remain unknown. In this study, we generated Sinorhizobium [...] Read more.

Symbiotic nitrogen fixation provides most of the nitrogen required for soybean growth. Rhizobial nodulation outer proteins (Nops) have been reported to influence host specificity during symbiosis establishment. However, the host proteins that interact with Nops remain unknown. In this study, we generated Sinorhizobium fredii HH103 mutants (HH103ΩNopL, HH103ΩNopT, and HH103ΩNopLΩNopT) and analysed the nodule number (NN) and nodule dry weight (NDW) of 12 soybean germplasms after inoculation with wild-type S. fredii HH103 or the mutant strains. The analysis of chromosome segment substitution lines revealed quantitative trait loci (QTLs) associated with NopL and NopT interactions. A total of 22 QTLs for the 2 nodule traits were detected and mapped to 12 different chromosomes in the soybean genome. Eight and fifteen QTLs were found to be associated with NN and NDW, respectively. Furthermore, 17 candidate genes were selected for further analyses. Considering the results of reverse-transcription quantitative PCR, we propose that the protein products of these 17 candidate genes interact with NopL and NopT. Full article

(This article belongs to the Special Issue Genetics Research and Molecular Breeding of Crops)

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19 pages, 11934 KiB

Open AccessArticle

Screening of Grain Development Heterosis Candidate Genes by Integrating QTL Mapping and RNA-Seq in Super Hybrid Rice WFYT025

by Tao Huang, Peng Wang, Yanning Wang, Shiying Huang, Qin Cheng, Caijing Li, Guangliang Wu, Qi Zhong, Mengmeng Yang, Haohua He and Jianmin Bian

Agronomy 2022, 12(4), 835; https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy12040835 - 29 Mar 2022

Viewed by 1726

Abstract

The application of heterosis during plant breeding increases rice grain yield. However, there have been limited studies on heterosis during rice grain development during the grain-filling stage; therefore, the genetic basis of heterosis for grain development during the grain-filling stage should be highly [...] Read more.

The application of heterosis during plant breeding increases rice grain yield. However, there have been limited studies on heterosis during rice grain development during the grain-filling stage; therefore, the genetic basis of heterosis for grain development during the grain-filling stage should be highly valued. In this study, a hybrid combination with the super hybrid rice WFYT025 was used to perform a transcriptomic dynamic analysis in grains at the beginning and middle grain-filling stages. A total of 1556 and 1507 transcripts that were differentially expressed between WFYT025 and its parents (DGHP) were identified at 1-day post-anthesis (DPA) and at 10 DPA, respectively. The analysis of the genetic effects of heterosis showed that the over-dominant effect (66.90% and 55.87%) was the main mode of action during grain development. The KEGG pathway and GO analysis of the DGHP indicated that the gibberellin biosynthetic, starch metabolic, and diterpenoid biosynthetic signaling pathways may be associated with heterosis during grain development. To further explore the candidate genes for grain development heterosis, a recombinant inbred line (RILs) population with a high-density genetic map of 2578 bin markers was constructed by crossing the parents of WFYT025, and nine stable QTLs for grain weight-related traits were identified. By comparing the DGHP with 20 QTLs, LOC_Os02g28820, LOC_Os02g32580, LOC_Os04g25440, and LOC_Os12g04980 were identified as grain development heterosis-related candidate genes. These findings provide resources for the study of heterosis during the grain development of super hybrid rice and provide valuable theoretical references for the cloning and functional analysis of heterosis-related genes. Full article

(This article belongs to the Special Issue Genetics Research and Molecular Breeding of Crops)

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