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21 pages, 10151 KiB

Open AccessArticle

Genome-Wide Association Study of Starch Properties in Local Thai Rice

by Parama Praphasanobol, Putut Rakhmad Purnama, Supaporn Junbuathong, Somsong Chotechuen, Peerapon Moung-Ngam, Waraluk Kasettranan, Chanita Paliyavuth, Luca Comai, Monnat Pongpanich, Teerapong Buaboocha and Supachitra Chadchawan

Plants 2023, 12(18), 3290; https://doi.org/10.3390/plants12183290 - 17 Sep 2023

Cited by 2 | Viewed by 1206

Abstract

Rice (Oryza sativa L.) is the main source of energy for humans and a staple food of high cultural significance for much of the world’s population. Rice with highly resistant starch (RS) is beneficial for health and can reduce the risk of [...] Read more.

Rice (Oryza sativa L.) is the main source of energy for humans and a staple food of high cultural significance for much of the world’s population. Rice with highly resistant starch (RS) is beneficial for health and can reduce the risk of disease, especially type II diabetes. The identification of loci affecting starch properties will facilitate breeding of high-quality and health-supportive rice. A genome-wide association study (GWAS) of 230 rice cultivars was used to identify candidate loci affecting starch properties. The apparent amylose content (AAC) among rice cultivars ranged from 7.04 to 33.06%, and the AAC was positively correlated with RS (R² = 0.94) and negatively correlated with rapidly available glucose (RAG) (R² = −0.73). Three loci responsible for starch properties were detected on chromosomes 1, 6, and 11. On chromosome 6, the most significant SNP corresponded to LOC_Os06g04200 which encodes granule-bound starch synthase I (GBSSI) or starch synthase. Two novel loci associated with starch traits were LOC_Os01g65810 and LOC_Os11g01580, which encode an unknown protein and a sodium/calcium exchanger, respectively. The markers associated with GBSSI and LOC_Os11g01580 were tested in two independent sets of rice populations to confirm their effect on starch properties. The identification of genes associated with starch traits will further the understanding of the molecular mechanisms affecting starch in rice and may be useful in the selection of rice varieties with improved starch. Full article

(This article belongs to the Special Issue Functional Genomics and Molecular Breeding of Crops)

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19 pages, 1481 KiB

Open AccessArticle

Molecular and Morphological Characterization of Introgression Lines with Resistance to Bacterial Leaf Blight and Blast in Rice

by Yasaswini Vishnu Priya Varanasi, Subhakara Rao Isetty, Padmashree Revadi, Divya Balakrishnan, Shaik Hajira, Madamsetty Srinivasa Prasad, Gouri Shankar Laha, Puvvada Perraju, Uma Maheshwar Singh, Vikas Kumar Singh, Arvind Kumar, Raman Meenakshi Sundaram and Jyothi Badri

Plants 2023, 12(16), 3012; https://doi.org/10.3390/plants12163012 - 21 Aug 2023

Viewed by 1056

Abstract

The present study evaluates marker assisted forward breeding (MAFB)-derived disease resistant introgression lines (ILs) which do not have the targeted resistance genes for bacterial blight (xa5 + xa13 + Xa21) and blast (Pi2 + Pi9 + Pi54). The ILs [...] Read more.

The present study evaluates marker assisted forward breeding (MAFB)-derived disease resistant introgression lines (ILs) which do not have the targeted resistance genes for bacterial blight (xa5 + xa13 + Xa21) and blast (Pi2 + Pi9 + Pi54). The ILs were derived in the background of two elite rice cultivars, Krishna Hamsa [Recurrent Parent 1 (RP1)] and WGL 14 (RP2), involving multi-parent inter-crossing. Molecular characterization with gene specific markers for seven reported resistance genes each for bacterial blight (Xa33, Xa38, xa23, Xa4, xa8, Xa27 and Xa41) and blast (Pi1, Pi20, Pi38, Pib, Pitp, Pizt and Pi40) revealed the presence of xa8 and Xa38, in addition to the targeted xa5, xa13 and Xa21 for bacterial blight resistance and Pi1, Pi38, Pi40, Pi20, Pib and Pipt, in addition to the targeted Pi9 and Pi54, for blast resistance in various combinations. A maximum of nine resistance genes xa5 + Xa21 + Pi54 + xa8 + Pipt + Pi38 + Pi1 + Pi20 + Pib was observed in RP1-IL 19030 followed by eight genes xa5 + xa13 + Xa21 + xa8 + Pi9 + Pipt + Pi1 + Pi20 in two RP2-ILs, 19344 and 19347. ANOVA revealed the presence of significant variability for all the yield traits except “days to 50% flowering” (DFF). Box plots depicted the seasonal differences in the phenotypic expression of the yield traits. There was significant positive association of grain yield with days to flowering, tiller number and panicle number. Thousand grain weight is also significantly and positively correlated with grain yield. On the contrary, grain yield showed a significantly negative association with plant height. Multi-parent selective inter-crossing in the present study not only led to the development of high yielding disease resistant ILs but also enhanced recovery of the recurrent parent via selection for essential morphological features. More than 90.0% genetic similarity in the ILs based on SNP-based background selection demonstrated the success of multi-parent selective intercrossing in the development of disease resistant NILs. Full article

(This article belongs to the Special Issue Functional Genomics and Molecular Breeding of Crops)

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23 pages, 5495 KiB

Open AccessArticle

Light-Induced TaHY5-7A and TaBBX-3B Physically Interact to Promote PURPLE PERICARP-MYB 1 Expression in Purple-Grained Wheat

by Qinqin Jiang, Wenhui Jiang, Ning Hu, Rui Tang, Yuxuan Dong, Hongqi Wu, Tianxiang Liu, Lulu Guan, Hanbing Zhang, Junbin Hou, Guaiqiang Chai and Zhonghua Wang

Plants 2023, 12(16), 2996; https://doi.org/10.3390/plants12162996 - 19 Aug 2023

Viewed by 1021

Abstract

Purple-grained wheat (Triticum aestivum L.) is an important germplasm source in crop breeding. Anthocyanin biosynthesis in the pericarps of purple-grained wheat is largely light-dependent; however, the regulatory mechanisms underlying light-induced anthocyanin accumulation in the wheat pericarp remain unknown. Here we determined that [...] Read more.

Purple-grained wheat (Triticum aestivum L.) is an important germplasm source in crop breeding. Anthocyanin biosynthesis in the pericarps of purple-grained wheat is largely light-dependent; however, the regulatory mechanisms underlying light-induced anthocyanin accumulation in the wheat pericarp remain unknown. Here we determined that anthocyanins rapidly accumulate in the pericarps of the purple-grained wheat cultivar Heixiaomai 76 (H76) at 16 days after pollination under light treatment. Using transcriptome sequencing, differential gene expression analysis, and phylogenetic analysis, we identified two key genes involved in light signaling in wheat: ELONGATED HYPOCOTYL 5-7A (TaHY5-7A) and B-BOX-3B (TaBBX-3B). TaHY5-7A and TaBBX-3B were highly expressed in purple-grained wheat pericarps. The heterologous expression of TaHY5-7A partially restored the phenotype of the Arabidopsis (Arabidopsis thaliana) hy5 mutant, resulting in increased anthocyanin accumulation and a shortened hypocotyl. The heterologous expression of TaBBX-3B in wild-type Arabidopsis had similar effects. TaHY5-7A and TaBBX-3B were nucleus-localized, consistent with a function in transcription regulation. However, TaHY5-7A, which lacks a transactivation domain, was not sufficient to activate the expression of PURPLE PERICARP-MYB 1 (TaPpm1), the key anthocyanin biosynthesis regulator in purple pericarps of wheat. TaHY5-7A physically interacted with TaBBX-3B in yeast two-hybrid and bimolecular fluorescence complementation assays. Additionally, TaHY5-7A, together with TaBBX-3B, greatly enhanced the promoter activity of TaPpm1 in a dual luciferase assay. Overall, our results suggest that TaHY5-7A and TaBBX-3B collaboratively activate TaPpm1 expression to promote light-induced anthocyanin biosynthesis in purple-pericarp wheat. Full article

(This article belongs to the Special Issue Functional Genomics and Molecular Breeding of Crops)

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11 pages, 5849 KiB

Open AccessCommunication

Composition and Structure of Arabidopsis thaliana Extrachromosomal Circular DNAs Revealed by Nanopore Sequencing

by Pavel Merkulov, Ekaterina Egorova and Ilya Kirov

Plants 2023, 12(11), 2178; https://doi.org/10.3390/plants12112178 - 30 May 2023

Cited by 6 | Viewed by 2214

Abstract

Extrachromosomal circular DNAs (eccDNAs) are enigmatic DNA molecules that have been detected in a range of organisms. In plants, eccDNAs have various genomic origins and may be derived from transposable elements. The structures of individual eccDNA molecules and their dynamics in response to [...] Read more.

Extrachromosomal circular DNAs (eccDNAs) are enigmatic DNA molecules that have been detected in a range of organisms. In plants, eccDNAs have various genomic origins and may be derived from transposable elements. The structures of individual eccDNA molecules and their dynamics in response to stress are poorly understood. In this study, we showed that nanopore sequencing is a useful tool for the detection and structural analysis of eccDNA molecules. Applying nanopore sequencing to the eccDNA molecules of epigenetically stressed Arabidopsis plants grown under various stress treatments (heat, abscisic acid, and flagellin), we showed that TE-derived eccDNA quantity and structure vary dramatically between individual TEs. Epigenetic stress alone did not cause eccDNA up-regulation, whereas its combination with heat stress triggered the generation of full-length and various truncated eccDNAs of the ONSEN element. We showed that the ratio between full-length and truncated eccDNAs is TE- and condition-dependent. Our work paves the way for further elucidation of the structural features of eccDNAs and their connections with various biological processes, such as eccDNA transcription and eccDNA-mediated TE silencing. Full article

(This article belongs to the Special Issue Functional Genomics and Molecular Breeding of Crops)

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13 pages, 5709 KiB

Open AccessArticle

Relocation of Sr48 to Chromosome 2D Using an Alternative Mapping Population and Development of a Closely Linked Marker Using Diverse Molecular Technologies

by Vallence Nsabiyera, Naeela Qureshi, Jianbo Li, Mandeep Randhawa, Peng Zhang, Kerrie Forrest, Urmil Bansal and Harbans Bariana

Plants 2023, 12(8), 1601; https://doi.org/10.3390/plants12081601 - 10 Apr 2023

Viewed by 1244

Abstract

The Ug99-effective stem rust resistance gene Sr48 was mapped to chromosome 2A based on its repulsion linkage with Yr1 in an Arina/Forno recombinant inbred line (RIL) population. Attempts to identify markers closely linked to Sr48 using available genomic resources were futile. This study [...] Read more.

The Ug99-effective stem rust resistance gene Sr48 was mapped to chromosome 2A based on its repulsion linkage with Yr1 in an Arina/Forno recombinant inbred line (RIL) population. Attempts to identify markers closely linked to Sr48 using available genomic resources were futile. This study used an Arina/Cezanne F_5:7 RIL population to identify markers closely linked with Sr48. Using the Arina/Cezanne DArTseq map, Sr48 was mapped on the short arm of chromosome 2D and it co-segregated with 12 markers. These DArTseq marker sequences were used for BlastN search to identify corresponding wheat chromosome survey sequence (CSS) contigs, and PCR-based markers were developed. Two simple sequence repeat (SSR) markers, sun590 and sun592, and two Kompetitive Allele-Specific PCR (KASP) markers were derived from the contig 2DS_5324961 that mapped distal to Sr48. Molecular cytogenetic analysis using sequential fluorescent in situ hybridization (FISH) and genomic in situ hybridization (GISH) identified a terminal translocation of chromosome 2A in chromosome 2DL of Forno. This translocation would have led to the formation of a quadrivalent involving chromosomes 2A and 2D in the Arina/Forno population, which would have exhibited pseudo-linkage between Sr48 and Yr1 in chromosome 2AL. Polymorphism of the closet marker sunKASP_239 among a set of 178 wheat genotypes suggested that this marker can be used for marker-assisted selection of Sr48. Full article

(This article belongs to the Special Issue Functional Genomics and Molecular Breeding of Crops)

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14 pages, 3729 KiB

Open AccessArticle

Generation of Wheat Near-Isogenic Lines Overexpressing 1Bx7 Glutenin with Increased Protein Contents and SDS-Sedimentation Values

by Myoung-Hui Lee, Changhyun Choi, Kyeong-Hoon Kim, Jae-Han Son, Go-Eun Lee, Jun-Yong Choi, Chon-Sik Kang, Jiyoung Shon, Jong-Min Ko and Kyeong-Min Kim

Plants 2023, 12(6), 1244; https://doi.org/10.3390/plants12061244 - 09 Mar 2023

Cited by 3 | Viewed by 1075

Abstract

Overexpression of Glu-1Bx7 via allele 1Bx7^OE significantly contributes to high dough strength in some wheat varieties and is useful for improving wheat quality. However, the proportion of wheat varieties containing Bx7^OE is quite low. In this study, four cultivars containing 1Bx7 [...] Read more.

Overexpression of Glu-1Bx7 via allele 1Bx7^OE significantly contributes to high dough strength in some wheat varieties and is useful for improving wheat quality. However, the proportion of wheat varieties containing Bx7^OE is quite low. In this study, four cultivars containing 1Bx7^OE were selected, and among the selected varieties, Chisholm (1Ax2*, 1Bx7^OE + 1By8*, and 1Dx5 + 1Dx10) was crossed with Keumkang, a wheat variety that contains 1Bx7 (1Ax2*, 1Bx7 + 1By8, and 1Dx5 + 1Dx10). SDS-PAGE and UPLC analyses showed that the expression of the high-molecular-weight glutenin subunit (HMW-GS) 1Bx7 was significantly higher in NILs (1Ax2*, 1Bx7^OE + 1By8*, and 1Dx5 + 1Dx10) compared with that in Keumkang. Wheat quality was analyzed with near infrared reflectance spectroscopy by measuring the protein content and SDS-sedimentation of NILs. The protein content of NILs (12.94%) was 21.65% higher than that of Chisholm (10.63%) and 4.54% higher than that of Keumkang (12.37%). In addition, the SDS-sedimentation value of NILs (44.29 mL) was 14.97% and 16.44% higher than that of Keumkang (38.52 mL) and Chisholm (38.03 mL), respectively. This study predicts that the quality of domestic wheat can be improved by crossbreeding with 1Bx7^OE-containing cultivars. Full article

(This article belongs to the Special Issue Functional Genomics and Molecular Breeding of Crops)

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11 pages, 1213 KiB

Open AccessCommunication

New Low Morphine Opium Poppy Genotype Obtained by TILLING Approach

by Jiří Červeň, Viktor Vrbovský, Jiří Horáček, Martin Bartas, Lenka Endlová, Petr Pečinka and Vladislav Čurn

Plants 2023, 12(5), 1077; https://doi.org/10.3390/plants12051077 - 28 Feb 2023

Cited by 1 | Viewed by 1814

Abstract

The opium poppy’s ability to produce various alkaloids is both useful and problematic. Breeding of new varieties with varying alkaloid content is therefore an important task. In this paper, the breeding technology of new low morphine poppy genotypes, based on a combination of [...] Read more.

The opium poppy’s ability to produce various alkaloids is both useful and problematic. Breeding of new varieties with varying alkaloid content is therefore an important task. In this paper, the breeding technology of new low morphine poppy genotypes, based on a combination of a TILLING approach and single-molecule real-time NGS sequencing, is presented. Verification of the mutants in the TILLING population was obtained using RT-PCR and HPLC methods. Only three of the single-copy genes of the morphine pathway among the eleven genes were used for the identification of mutant genotypes. Point mutations were obtained only in one gene (CNMT) while an insertion was obtained in the other (SalAT). Only a few expected transition SNPs from G:C to A:T were obtained. In the low morphine mutant genotype, the production of morphine was decreased to 0.1% from 1.4% in the original variety. A comprehensive description of the breeding process, a basic characterization of the main alkaloid content, and a gene expression profile for the main alkaloid-producing genes is provided. Difficulties with the TILLING approach are also described and discussed. Full article

(This article belongs to the Special Issue Functional Genomics and Molecular Breeding of Crops)

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15 pages, 2525 KiB

Open AccessArticle

QTL Analysis Reveals Conserved and Differential Genetic Regulation of Maize Lateral Angles above the Ear

by Yanbin Zhu, Bo Song, Yanling Guo, Baobao Wang, Changcheng Xu, Hongyu Zhu, Lizhu E, Jinsheng Lai, Weibin Song and Haiming Zhao

Plants 2023, 12(3), 680; https://doi.org/10.3390/plants12030680 - 03 Feb 2023

Viewed by 1720

Abstract

Improving the density tolerance and planting density has great importance for increasing maize production. The key to promoting high density planting is breeding maize with a compact canopy architecture, which is mainly influenced by the angles of the leaves and tassel branches above [...] Read more.

Improving the density tolerance and planting density has great importance for increasing maize production. The key to promoting high density planting is breeding maize with a compact canopy architecture, which is mainly influenced by the angles of the leaves and tassel branches above the ear. It is still unclear whether the leaf angles of different stem nodes and tassel branches are controlled by similar genetic regulatory mechanisms, which limits the ability to breed for density-tolerant maize. Here, we developed a population with 571 double haploid lines derived from inbred lines, PHBA6 and Chang7-2, showing significant differences in canopy architecture. Phenotypic and QTL analyses revealed that the genetic regulation mechanism was largely similar for closely adjacent leaves above the ears. In contrast, the regulation mechanisms specifying the angles of distant leaves and the angles of leaves vs. tassel branches are largely different. The liguless1 gene was identified as a candidate gene for QTLs co-regulating the angles of different leaves and the tassel branch, consistent with its known roles in regulating plant architecture. Our findings can be used to develop strategies for the improvement of leaf and tassel architecture through the introduction of trait-specific or pleiotropic genes, thus benefiting the breeding of maize with increased density tolerance in the future. Full article

(This article belongs to the Special Issue Functional Genomics and Molecular Breeding of Crops)

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13 pages, 1779 KiB

Open AccessArticle

Molecular Characterization and Efficacy Evaluation of Transgenic Maize Harboring cry2Ab-vip3A-cp4epsps for Insect Resistance and Herbicide Tolerance

by Fantao Liu, Yuan Liu, Junjie Zou, Lan Zhang, Hongyan Zheng, Yanzhong Luo, Xiaoping Wang and Lei Wang

Plants 2023, 12(3), 612; https://doi.org/10.3390/plants12030612 - 30 Jan 2023

Viewed by 2105

Abstract

Insect infestation and weed interference have a seriously negative impact on the growth, yield, and grain quality of maize. In this study, transgenic maize plants harboring three exogenous genes, cry2Ab, vip3A, and cp4epsps, that were constructed into a single T-DNA [...] Read more.

Insect infestation and weed interference have a seriously negative impact on the growth, yield, and grain quality of maize. In this study, transgenic maize plants harboring three exogenous genes, cry2Ab, vip3A, and cp4epsps, that were constructed into a single T-DNA were developed for protection against insects and weeds. The transgene integration sites on the chromosomes in two transgenic maize events, CVC-1 and CVC-2, were determined using whole genome sequencing and specific PCR detection. As revealed by laboratory insect bioassays, these two transgenic events exhibited strong insecticidal toxicity against three major species of Lepidoptera insects, including Mythimna separata, Helicoverpa armigera, and Spodoptera frugiperda, with mortality rates exceeding 96%, 100%, and 100%, respectively, after six days of infestation. In addition, CVC-1 exhibited a high tolerance to glyphosate under field conditions. The successful expressions of cry2Ab, vip3A, and cp4epsps in various tissues at different developmental stages of CVC-1 were validated at the transcriptional and translational levels using quantitative real-time reverse transcription PCR (qRT-PCR) and enzyme-linked immunosorbent assay (ELISA), respectively. These findings demonstrated that the transgenic maize CVC-1 developed using this triple gene construct has excellent insect resistance and herbicide tolerance, which may provide a valuable germplasm resource and data support for future maize breeding of insect and weed control. Full article

(This article belongs to the Special Issue Functional Genomics and Molecular Breeding of Crops)

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18 pages, 3511 KiB

Open AccessArticle

Genome-Wide Identification and Analysis of the Maize Serine Peptidase S8 Family Genes in Response to Drought at Seedling Stage

by Hongwei Cui, Guyi Zhou, Hongqiang Ruan, Jun Zhao, Agula Hasi and Na Zong

Plants 2023, 12(2), 369; https://doi.org/10.3390/plants12020369 - 12 Jan 2023

Cited by 2 | Viewed by 1717

Abstract

Subtilisin-like proteases (subtilases) are found in almost all plant species and are involved in regulating various biotic and abiotic stresses. Although the literature on subtilases in different plant species is vast, the gene function of the serine peptidase S8 family and its maize [...] Read more.

Subtilisin-like proteases (subtilases) are found in almost all plant species and are involved in regulating various biotic and abiotic stresses. Although the literature on subtilases in different plant species is vast, the gene function of the serine peptidase S8 family and its maize subfamily is still unknown. Here, a bioinformatics analysis of this gene family was conducted by describing gene structure, conserved motifs, phylogenetic relationships, chromosomal distributions, gene duplications, and promoter cis-elements. In total, we identified 18 ZmSPS8 genes in maize, distributed on 7 chromosomes, and half of them were hydrophilic. Most of these proteins were located at the cell wall and had similar secondary and tertiary structures. Prediction of cis-regulatory elements in promoters illustrated that they were mainly associated with hormones and abiotic stress. Maize inbred lines B73, Zheng58, and Qi319 were used to analyze the spatial-temporal expression patterns of ZmSPS8 genes under drought treatment. Seedling drought results showed that Qi319 had the highest percent survival after 14 d of withholding irrigation, while B73 was the lowest. Leaf relative water content (LRWC) declined more rapidly in B73 and to lower values, and the nitrotetrazolium blue chloride (NBT) contents of leaves were higher in Qi319 than in the other inbreds. The qPCR results indicated that 6 serine peptidase S8 family genes were positively or negatively correlated with plant tolerance to drought stress. Our study provides a detailed analysis of the ZmSPS8s in the maize genome and finds a link between drought tolerance and the family gene expression, which was established by using different maize inbred lines. Full article

(This article belongs to the Special Issue Functional Genomics and Molecular Breeding of Crops)

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15 pages, 3000 KiB

Open AccessArticle

Effects of Insect-Resistant Maize HGK60 on Community Diversity of Bacteria and Fungi in Rhizosphere Soil

by Yinxiao Wang, Mingjun Zhang, Shengyan Li, Pengcheng Li and Zhihong Lang

Plants 2022, 11(21), 2824; https://doi.org/10.3390/plants11212824 - 24 Oct 2022

Cited by 2 | Viewed by 1214

Abstract

The influence of biotech crops on microbial communities in rhizosphere soil is an important issue in biosafety assessments. The transgenic maize HGK60 harboring the Bt cry1Ah gene enhanced the resistance to lepidopteran pests, while the ecological risk of HGK60 maize on rhizosphere microorganisms [...] Read more.

The influence of biotech crops on microbial communities in rhizosphere soil is an important issue in biosafety assessments. The transgenic maize HGK60 harboring the Bt cry1Ah gene enhanced the resistance to lepidopteran pests, while the ecological risk of HGK60 maize on rhizosphere microorganisms is unclear. In this study, we comprehensively analyzed the diversity and composition of bacterial and fungal communities in the rhizosphere soil around Bt maize HGK60 and the near-isogenic non-Bt maize ZD958 at four growth stages via a high-throughput sequencing technique. The results showed that HGK60 maize unleashed temporary effects on the bacterial and fungal diversity and richness during the study plant’s development, which would be restored after one cycle of plant cultivation due to the application of the same agricultural management. The differences of bacterial and fungal communities were marked by seasonality, while the different growth stage was the important factor as opposed to the cultivar contributing to the shifts in the bacterial and fungal communities’ structure. This study will provide useful information regarding the impact of Bt transgenic maize on the soil microbiome and a theoretical basis for the development of a safety assessment approach for Bt maize in China. Full article

(This article belongs to the Special Issue Functional Genomics and Molecular Breeding of Crops)

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11 pages, 1739 KiB

Open AccessArticle

Genome-Wide Association Study Reveals the Genetic Basis of Kernel and Cob Moisture Changes in Maize at Physiological Maturity Stage

by Minyan Zhang, Chaoyang Xiangchen, Jiaquan Yan, Yujuan Chengxu, Hao Liu, Chaoying Zou, Guangtang Pan, Yaou Shen and Langlang Ma

Plants 2022, 11(15), 1989; https://doi.org/10.3390/plants11151989 - 30 Jul 2022

Cited by 1 | Viewed by 1313

Abstract

Low moisture content (MC) and high dehydration rate (DR) at physiological maturity affect grain mechanical harvest, transport, and storage. In this study, we used an association panel composed of 241 maize inbred lines to analyze ear moisture changes at physiological maturity stage. A [...] Read more.

Low moisture content (MC) and high dehydration rate (DR) at physiological maturity affect grain mechanical harvest, transport, and storage. In this study, we used an association panel composed of 241 maize inbred lines to analyze ear moisture changes at physiological maturity stage. A genome-wide association study revealed nine significant SNPs and 91 candidate genes. One SNP (SYN38588) was repeatedly detected for two traits, and 15 candidate genes were scanned in the linkage disequilibrium regions of this SNP. Of these, genes Zm00001d020615 and Zm00001d020623 were individually annotated as a polygalacturonase (PG) and a copper transporter 5.1 (COPT5.1), respectively. Candidate gene association analysis showed that three SNPs located in the exons of Zm00001d020615 were significantly associated with the dehydration rate, and AATTAA was determined as the superior haplotype. All these findings suggested that Zm00001d020615 was a key gene affecting moisture changes of maize at the physiological maturity stage. These results have demonstrated the genetic basis of ear moisture changes in maize and indicated a superior haplotype for cultivating maize varieties with low moisture content and high dehydration rates. Full article

(This article belongs to the Special Issue Functional Genomics and Molecular Breeding of Crops)

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20 pages, 3769 KiB

Open AccessArticle

SlHSP17.7 Ameliorates Chilling Stress-Induced Damage by Regulating Phosphatidylglycerol Metabolism and Calcium Signal in Tomato Plants

by Yuanyuan Wu, Shuwen Lv, Yaran Zhao, Chenliang Chang, Wei Hong and Jing Jiang

Plants 2022, 11(14), 1865; https://doi.org/10.3390/plants11141865 - 18 Jul 2022

Cited by 3 | Viewed by 1743

Abstract

Tomatoes (Solanum lycopersicum L.) are sensitive to chilling temperatures between 0 °C and 12 °C owing to their tropical origin. SlHSP17.7, a cytoplasmic heat shock protein, interacts with cation/calcium exchanger 1-like (SlCCX1-like) protein and promotes chilling tolerance in tomato fruits (Zhang, et [...] Read more.

Tomatoes (Solanum lycopersicum L.) are sensitive to chilling temperatures between 0 °C and 12 °C owing to their tropical origin. SlHSP17.7, a cytoplasmic heat shock protein, interacts with cation/calcium exchanger 1-like (SlCCX1-like) protein and promotes chilling tolerance in tomato fruits (Zhang, et al., Plant Sci., 2020, 298, 1–12). The overexpression of SlHSP17.7 can also promote cold tolerance in tomato plants, but its specific mechanism remains unclear. In this study, we show that the overexpression of SlHSP17.7 in tomato plants enhances chilling tolerance with better activity of photosystem II (PSII). Metabolic analyses revealed that SlHSP17.7 improved membrane fluidity by raising the levels of polyunsaturated fatty acids. Transcriptome analyses showed that SlHSP17.7 activated Ca²⁺ signaling and induced the expression of C-repeat binding factor (CBF) genes, which in turn inhibited the production of reactive oxygen species (ROS). The gene coexpression network analysis showed that SlHSP17.7 is coexpressed with SlMED26b. SlMED26b silencing significantly lowered OE-HSP17.7 plants’ chilling tolerance. Thus, SlHSP17.7 modulates tolerance to chilling via both membrane fluidity and Ca²⁺-mediated CBF pathway in tomato plants. Full article

(This article belongs to the Special Issue Functional Genomics and Molecular Breeding of Crops)

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14 pages, 2883 KiB

Open AccessArticle

PNGSeqR: An R Package for Rapid Candidate Gene Selection through Pooled Next-Generation Sequencing

by Sihan Zhen, Hongwei Zhang, Yuxin Xie, Song Zhang, Yan Chen, Riliang Gu, Sanzhen Liu, Xuemei Du and Junjie Fu

Plants 2022, 11(14), 1821; https://doi.org/10.3390/plants11141821 - 11 Jul 2022

Viewed by 1773

Abstract

Although bulked segregant analysis (BSA) has been used extensively in genetic mapping, user-friendly tools which can integrate current algorithms for researchers with no background in bioinformatics are scarce. To address this issue, we developed an R package, PNGSeqR, which takes single-nucleotide polymorphism (SNP) [...] Read more.

Although bulked segregant analysis (BSA) has been used extensively in genetic mapping, user-friendly tools which can integrate current algorithms for researchers with no background in bioinformatics are scarce. To address this issue, we developed an R package, PNGSeqR, which takes single-nucleotide polymorphism (SNP) markers from next-generation sequencing (NGS) data in variant call format (VCF) as the input file, provides four BSA algorithms to indicate the magnitude of genome-wide signals, and rapidly defines the candidate region through the permutation test and fractile quantile. Users can choose the analysis methods according to their data and experimental design. In addition, it also supports differential expression gene analysis (DEG) and gene ontology analysis (GO) to prioritize the target gene. Once the analysis is completed, the plots can conveniently be exported. Full article

(This article belongs to the Special Issue Functional Genomics and Molecular Breeding of Crops)

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11 pages, 1834 KiB

Open AccessFeature PaperArticle

OsBSK3 Positively Regulates Grain Length and Weight by Inhibiting the Phosphatase Activity of OsPPKL1

by Peng Tian, Jiafan Liu, Baohui Yan, Shuai Li, Bin Lei, Rongxin Shen, Cailin Lei and Miaoyun Xu

Plants 2022, 11(12), 1586; https://doi.org/10.3390/plants11121586 - 16 Jun 2022

Cited by 6 | Viewed by 1631

Abstract

Brassinosteroids (BRs) are a crucial class of plant hormones that regulate many important agronomic traits in rice (Oryza sativa L.); thus, the BR signaling pathway is a very important tool for breeders to improve the grain yield and quantity of rice. Contrary [...] Read more.

Brassinosteroids (BRs) are a crucial class of plant hormones that regulate many important agronomic traits in rice (Oryza sativa L.); thus, the BR signaling pathway is a very important tool for breeders to improve the grain yield and quantity of rice. Contrary to the well-established BR signaling pathway in Arabidopsis, there are significant gaps in the rice BR signaling pathway, especially the regulation mechanism from OsBSK3 to OsPPKLs and OsGSKs. In this study, we report how OsBSK3 knockout mutants confer shorter and lighter grains and exhibit a typical BR-insensitive phenotype, suggesting OsBSK3 plays a positive role in BR signaling without genetic redundancy with homologs. Furthermore, OsBSK3 could physically interact with OsPPKL1 and OsGSK3, the downstream components in BR signaling, as a scaffold protein, and inhibit the phosphatase activity of OsPPKL1 on the dephosphorylation of OsGSK3. In addition, the genetic evidence showed OsBSK3 acts upstream of OsPPKL1 in regulating grain length and weight. Our results clarify the role of OsBSK3 and provide new insights into BR-signaling mechanisms, leading to potential new targets for the genetic improvement of rice. Full article

(This article belongs to the Special Issue Functional Genomics and Molecular Breeding of Crops)

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Review

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20 pages, 561 KiB

Open AccessReview

Orchard Management and Incorporation of Biochemical and Molecular Strategies for Improving Drought Tolerance in Fruit Tree Crops

by Sama Rahimi Devin, Ángela S. Prudencio, Sayyed Mohammad Ehsan Mahdavi, Manuel Rubio, Pedro J. Martínez-García and Pedro Martínez-Gómez

Plants 2023, 12(4), 773; https://doi.org/10.3390/plants12040773 - 08 Feb 2023

Cited by 7 | Viewed by 2690

Abstract

Water scarcity is one of the greatest concerns for agronomy worldwide. In recent years, many water resources have been depleted due to multiple factors, especially mismanagement. Water resource shortages lead to cropland expansion, which likely influences climate change and affects global agriculture, especially [...] Read more.

Water scarcity is one of the greatest concerns for agronomy worldwide. In recent years, many water resources have been depleted due to multiple factors, especially mismanagement. Water resource shortages lead to cropland expansion, which likely influences climate change and affects global agriculture, especially horticultural crops. Fruit yield is the final aim in commercial orchards; however, drought can slow tree growth and/or decrease fruit yield and quality. It is therefore necessary to find approaches to solve this problem. The main objective of this review is to discuss the most recent horticultural, biochemical, and molecular strategies adopted to improve the response of temperate fruit crops to water stress. We also address the viability of cultivating fruit trees in dry areas and provide precise protection methods for planting fruit trees in arid lands. We review the main factors involved in planting fruit trees in dry areas, including plant material selection, regulated deficit irrigation (DI) strategies, rainwater harvesting (RWH), and anti-water stress materials. We also provide a detailed analysis of the molecular strategies developed to combat drought, such as Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) through gene overexpression or gene silencing. Finally, we look at the molecular mechanisms associated with the contribution of the microbiome to improving plant responses to drought. Full article

(This article belongs to the Special Issue Functional Genomics and Molecular Breeding of Crops)

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