Topic Editors

Center of Crop Germplasm Innovation & Utilization, Huazhi Bio-Tech Co., Ltd., Changsha 410125, China
Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126 Milan, Italy

Plant Domestication and Crop Evolution

Abstract submission deadline
closed (31 January 2023)
Manuscript submission deadline
closed (31 March 2023)
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Topic Information

Dear Colleagues,

Domestication is a good model for the study of evolutionary processes because of the recent evolution of crop species (~12,000 years ago), the key role of selection in their origins, and good archaeological and historical data on their spread and diversification. Domestication has a profound impact on crops. In the past 20 years, the genetic structure of crop domestication and the selection characteristics of domesticated species have been the foci of molecular genetics research. Today, with the development of genomic techniques, genomics are widely applied to crop domestication studies, which has significantly accelerated our understanding of genetic diversity and molecular evolution. In addition, genomic technologies have also provided support for studies on plant domestication and crop evolution.

This Topic aims at promoting discussions on the issues of plant domestication research, including (but not limited to) the following issues:

  • The geography of plant domestication;
  • The time frame and pace of plant domestication;
  • The genetic or genomic basis for domestication.

Dr. Junhua Peng
Dr. Fabrizio Grassi
Topic Editors

Keywords

  • crop evolution
  • crop wild relatives
  • domestication syndrome
  • genetic diversity
  • crop domestication
  • convergent evolution
  • natural selection
  • population genomics

Participating Journals

Journal Name Impact Factor CiteScore Launched Year First Decision (median) APC
Agronomy
agronomy
3.7 5.2 2011 15.8 Days CHF 2600
Diversity
diversity
2.4 3.1 2009 17.8 Days CHF 2600
Genes
genes
3.5 5.1 2010 16.5 Days CHF 2600
International Journal of Molecular Sciences
ijms
5.6 7.8 2000 16.3 Days CHF 2900
Plants
plants
4.5 5.4 2012 15.3 Days CHF 2700

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Published Papers (15 papers)

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13 pages, 2012 KiB  
Article
The Lesson Learned from the Unique Evolutionary Story of Avirulence Gene AvrPii of Magnaporthe oryzae
by Xing Wang, Weihuai Wu, Yaling Zhang, Cheng Li, Jinyan Wang, Jianqiang Wen, Shulin Zhang, Yongxiang Yao, Weisheng Lu, Zhenghong Zhao, Jiasui Zhan and Qinghua Pan
Genes 2023, 14(5), 1065; https://doi.org/10.3390/genes14051065 - 11 May 2023
Cited by 1 | Viewed by 1267
Abstract
Blast, caused by Magnaporthe oryzae, is one of the most destructive diseases affecting rice production. Understanding population dynamics of the pathogen’s avirulence genes is pre-required for breeding and then deploying new cultivars carrying promising resistance genes. The divergence and population structure of [...] Read more.
Blast, caused by Magnaporthe oryzae, is one of the most destructive diseases affecting rice production. Understanding population dynamics of the pathogen’s avirulence genes is pre-required for breeding and then deploying new cultivars carrying promising resistance genes. The divergence and population structure of AvrPii was dissected in the populations of southern (Guangdong, Hunan, and Guizhou) and northern (Jilin, Liaoning, and Heilongjiang) China, via population genetic and evolutionary approaches. The evolutionary divergence between a known haplotype AvrPii-J and a novel one AvrPii-C was demonstrated by haplotype-specific amplicon-based sequencing and genetic transformation. The different avirulent performances of a set of seven haplotype-chimeric mutants suggested that the integrity of the full-length gene structures is crucial to express functionality of individual haplotypes. All the four combinations of phenotypes/genotypes were detected in the three southern populations, and only two in the northern three, suggesting that genic diversity in the southern region was higher than those in the northern one. The population structure of the AvrPii family was shaped by balancing, purifying, and positive selection pressures in the Chinese populations. The AvrPii-J was recognized as the wild type that emerged before rice domestication. Considering higher frequencies of avirulent isolates were detected in Hunan, Guizhou, and Liaoning, the cognate resistance gene Pii could be continuously used as a basic and critical resistance resource in such regions. The unique population structures of the AvrPii family found in China have significant implications for understanding how the AvrPii family has kept an artful balance and purity among its members (haplotypes) those keenly interact with Pii under gene-for-gene relationships. The lesson learned from case studies on the AvrPii family is that much attention should be paid to haplotype divergence of target gene. Full article
(This article belongs to the Topic Plant Domestication and Crop Evolution)
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12 pages, 946 KiB  
Review
Molecular Mechanisms of the Co-Evolution of Wheat and Rust Pathogens
by Emmanuel N. Annan and Li Huang
Plants 2023, 12(9), 1809; https://doi.org/10.3390/plants12091809 - 28 Apr 2023
Viewed by 1881
Abstract
Wheat (Triticum spp.) is a cereal crop domesticated >8000 years ago and the second-most-consumed food crop nowadays. Ever since mankind has written records, cereal rust diseases have been a painful awareness in antiquity documented in the Old Testament (about 750 B.C.). The [...] Read more.
Wheat (Triticum spp.) is a cereal crop domesticated >8000 years ago and the second-most-consumed food crop nowadays. Ever since mankind has written records, cereal rust diseases have been a painful awareness in antiquity documented in the Old Testament (about 750 B.C.). The pathogen causing the wheat stem rust disease is among the first identified plant pathogens in the 1700s, suggesting that wheat and rust pathogens have co-existed for thousands of years. With advanced molecular technologies, wheat and rust genomes have been sequenced, and interactions between the host and the rust pathogens have been extensively studied at molecular levels. In this review, we summarized the research at the molecular level and organized the findings based on the pathogenesis steps of germination, penetration, haustorial formation, and colonization of the rusts to present the molecular mechanisms of the co-evolution of wheat and rust pathogens. Full article
(This article belongs to the Topic Plant Domestication and Crop Evolution)
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18 pages, 7111 KiB  
Article
Molecular Analysis of Genetic Diversity and Structure of the Lablab (Lablab purpureus (L.) Sweet) Gene Pool Reveals Two Independent Routes of Domestication
by Alisa Kongjaimun, Yu Takahashi, Yosuke Yoshioka, Norihiko Tomooka, Rachsawan Mongkol and Prakit Somta
Plants 2023, 12(1), 57; https://doi.org/10.3390/plants12010057 - 22 Dec 2022
Cited by 7 | Viewed by 1625
Abstract
In this study, genetic diversity and structure of 474 cultivated and 19 wild lablab (Lablab purpureus) accessions. were determined using 15 nuclear and 6 chloroplast SSR markers. The overall gene diversity was relatively low (0.3441). Gene diversity in the wild accessions [...] Read more.
In this study, genetic diversity and structure of 474 cultivated and 19 wild lablab (Lablab purpureus) accessions. were determined using 15 nuclear and 6 chloroplast SSR markers. The overall gene diversity was relatively low (0.3441). Gene diversity in the wild accessions (0.6059) was about two-folds greater than that in the cultivated accessions. In the wild accessions, gene diversity was greatest in the southern Africa, followed by East Africa. In the cultivated accessions, gene diversity was highest in the eastern Africa. The results suggested that South Africa is the center of origin and East Africa is the center of domestication of lablab. Different cluster analyses showed that 2-seeded-pod cultivated accessions (ssp. uncinatus) were clustered with wild accessions and that 4–(6)-seeded-pod cultivated accessions (ssp. purpureus and bengalensis) were intermingled. UPGMA tree suggested that ssp. purpureus and bengalensis were domesticated from 4-seeded-pod wild accessions of southern Africa. Haplotype network analysis based on nuclear SSRs revealed two domestication routes; the ssp. uncinatus is domesticated from 2-seeded-pod wild lablab (wild spp. uncinatus) from East Africa (Ethiopia), while the ssp. purpureus and bengalensis are domesticated from 4-seeded-pod wild lablab from Central Africa (Rwanda). These results are useful for understanding domestication and revising classification of lablab. Full article
(This article belongs to the Topic Plant Domestication and Crop Evolution)
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18 pages, 3086 KiB  
Article
Tracing Back the History of Pepper (Capsicum annuum) in the Iberian Peninsula from a Phenomics Point of View
by Cristina Silvar, Filomena Rocha and Ana M. Barata
Plants 2022, 11(22), 3075; https://doi.org/10.3390/plants11223075 - 13 Nov 2022
Cited by 1 | Viewed by 2243
Abstract
The Iberian Peninsula was the place where pepper (Capsicum annuum) entered Europe and dispersed to other continents but was also an important secondary center for its diversification. The current work evaluated the phenotypic diversity existing in this region and investigated how [...] Read more.
The Iberian Peninsula was the place where pepper (Capsicum annuum) entered Europe and dispersed to other continents but was also an important secondary center for its diversification. The current work evaluated the phenotypic diversity existing in this region and investigated how that evolved from Capsicum native areas (Mexico and Andean Region). For that purpose, the high-throughput phenotyping tool Tomato Analyzer was employed. Descriptors related to size and shape were the most distinctive among fruit types, reflecting a broad diversity for Iberian peppers. These traits likely reflected those suffering from more intensive human selections, driving the worldwide expansion of C. annuum. Iberian peppers maintained close proximity to the American accessions in terms of fruit phenomics. The highest similarities were observed for those coming from the southeastern edge of the Peninsula, while northwestern accessions displayed more significant differences. Common fruit traits (small, conical) suggested that Portuguese and Spanish landraces may have arisen from an ancient American population that entered the south of Spain and promptly migrated to the central and northern territories, giving rise to larger, elongated, and blocky pods. Such lineages would be the result of adaptations to local soil–climate factors prevailing in different biogeographic provinces. Full article
(This article belongs to the Topic Plant Domestication and Crop Evolution)
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16 pages, 2965 KiB  
Article
Comparative Transcriptome Analysis Identifies Key Defense Genes and Mechanisms in Mulberry (Morus alba) Leaves against Silkworms (Bombyx mori)
by Xuejie Zhang, Xinxin Zhu, Yuqian Zhang, Zhicheng Wu, Shoujin Fan and Luoyan Zhang
Int. J. Mol. Sci. 2022, 23(21), 13519; https://doi.org/10.3390/ijms232113519 - 04 Nov 2022
Cited by 2 | Viewed by 1620
Abstract
As a consequence of long-term coevolution and natural selection, the leaves of mulberry (Morus alba) trees have become the best food source for silkworms (Bombyx mori). Nevertheless, the molecular and genomic basis of defense response remains largely unexplored. In [...] Read more.
As a consequence of long-term coevolution and natural selection, the leaves of mulberry (Morus alba) trees have become the best food source for silkworms (Bombyx mori). Nevertheless, the molecular and genomic basis of defense response remains largely unexplored. In the present study, we assessed changes in the transcriptome changes of mulberry in response to silkworm larval feeding at 0, 3, and 6 h. A total of 4709 (up = 2971, down = 1738) and 3009 (up = 1868, down = 1141) unigenes were identified after 3 and 6 h of silkworm infestation, respectively. MapMan enrichment analysis results show structural traits such as leaf surface wax, cell wall thickness and lignification form the first physical barrier to feeding by the silkworms. Cluster analysis revealed six unique temporal patterns of transcriptome changes. We predicted that mulberry promoted rapid changes in signaling and other regulatory processes to deal with mechanical damage, photosynthesis impairment, and other injury caused by herbivores within 3–6 h. LRR-RK coding genes (THE1, FER) was predicted participated in perception of cell wall perturbation in mulberry responding to silkworm feeding. Ca2+ signal sensors (CMLs), ROS (OST1, SOS3), RBOHD/F, CDPKs, and ABA were part of the regulatory network after silkworm feeding. Jasmonic acid (JA) signal transduction was predicted to act in silkworm feeding response, 10 JA signaling genes (such as OPR3, JAR1, and JAZ1) and 21 JA synthesis genes (such as LOX2, AOS, and ACX1) were upregulated after silkworm feeding for 3 h. Besides, genes of “alpha-Linolenic acid metabolism” and “phenylpropanoid biosynthesis” were activated in 3 h to reprogram secondary metabolism. Collectively, these findings provided valuable insights into silkworm herbivory-induced regulatory and metabolic processes in mulberry, which might help improve the coevolution of silkworm and mulberry. Full article
(This article belongs to the Topic Plant Domestication and Crop Evolution)
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15 pages, 2567 KiB  
Article
Domestication Syndrome in Dacryodes edulis (Burseraceae): Comparison of Morphological and Biochemical Traits between Wild and Cultivated Populations
by Franca Marcelle Meguem Mboujda, Marie-Louise Avana-Tientcheu, Stéphane Takoudjou Momo, Alix Mboukap Ntongme, Virginie Vaissayre, Laura N. Azandi, Stéphane Dussert, Hilaire Womeni, Jean-Michel Onana, Bonaventure Sonké, Christopher Tankou and Jérôme Duminil
Plants 2022, 11(19), 2496; https://doi.org/10.3390/plants11192496 - 23 Sep 2022
Cited by 4 | Viewed by 1763
Abstract
For millennia, people have harvested fruits from the wild for their alimentation. Gradually, they have started selecting wild individuals presenting traits of interest, protecting and cultivating them. This was the starting point of their domestication. The passage from a wild to a cultivated [...] Read more.
For millennia, people have harvested fruits from the wild for their alimentation. Gradually, they have started selecting wild individuals presenting traits of interest, protecting and cultivating them. This was the starting point of their domestication. The passage from a wild to a cultivated status is accompanied by a modification of a number of morphological and genetic traits, commonly known as the domestication syndrome. We studied the domestication syndrome in Dacryodes edulis (G.Don) H.J.Lam (known as ‘African plum’ or ‘safoutier/prunier’), a socio-economically important indigenous fruit tree species in West and Central Africa. We compared wild and cultivated individuals for their sex distribution; flower, fruit and seed morphometric characteristics; seed germination temporal dynamic and fruit lipid composition. We found a higher percentage of male and male-hermaphrodite sexual types in wild populations than in cultivated ones; a lower fruit and seed mass in wild individuals; and similar mean time of germination, oil content and fatty acid composition between wild and cultivated individuals. Our results are interpreted in light of the presence of a domestication syndrome in D. edulis. Full article
(This article belongs to the Topic Plant Domestication and Crop Evolution)
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15 pages, 1320 KiB  
Article
Jatropha curcas L. as a Plant Model for Studies on Vegetative Propagation of Native Forest Plants
by Renato Lustosa Sobrinho, Tiago Zoz, Taciane Finato, Carlos Eduardo da Silva Oliveira, Sebastião Soares de Oliveira Neto, André Zoz, Ibrahim A. Alaraidh, Mohammad K. Okla, Yasmeen A. Alwasel, Gerrit Beemster and Hamada AbdElgawad
Plants 2022, 11(19), 2457; https://doi.org/10.3390/plants11192457 - 21 Sep 2022
Cited by 4 | Viewed by 2147
Abstract
Even though it is a forest native plant, there are already several studies evaluating the small genome of Jatropha curcas L., which belongs to the Euphorbiaceae family, and may be an excellent representative model for the other plants from the same family. Jatropha [...] Read more.
Even though it is a forest native plant, there are already several studies evaluating the small genome of Jatropha curcas L., which belongs to the Euphorbiaceae family, and may be an excellent representative model for the other plants from the same family. Jatropha curcas L. plant has fast growth, precocity, and great adaptability, facilitating silvicultural studies, allowing important information to be obtained quickly, and reducing labor costs. This information justifies the use of the species as a model plant in studies involving the reproduction of native plants. This study aimed to evaluate the possibility of using Jatropha curcas L. as a model plant for studies involving native forest plants and establish possible recommendations for the vegetative propagation of the species using hardwood cuttings. The information collected can be helpful to other native forest plant species, similar to Jatropha curcas L. To this end, the effects of hardwood cutting length (10, 20, and 30 cm) and the part of the hardwood cuttings (basal, middle, and apex) were evaluated. Moreover, the influence of immersing the hardwood cuttings in solutions containing micronutrients (boron or zinc) or plant regulators (2,4-D, GA3) and a biostimulant composed of kinetin (0.09 g L−1), gibberellic acid (0.05 g L−1), and 4-indole-3-butyric acid (0.05 g L−1). The experiments were carried out in duplicates. In one duplicate, sand was used as the substrate, and rooting evaluations were made 77 days after planting. In another duplicate, a substrate composed of 50% soil, 40% poultry litter, and 10% sand was used, and the evaluations of the saplings were performed 120 days after planting. The GA3 solutions inhibited the roots’ and sprouts’ emissions, while immersion in 2,4-D solution increased the number of primary roots at 77 days after planting. The hardwood cuttings from the basal part of the branch had the best results for producing saplings. Full article
(This article belongs to the Topic Plant Domestication and Crop Evolution)
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17 pages, 2507 KiB  
Article
Transcriptome Analysis Reveals Molecular Mechanisms under Salt Stress in Leaves of Foxtail Millet (Setaria italica L.)
by Fei Han, Mingjie Sun, Wei He, Shuqing Guo, Jingyi Feng, Hui Wang, Quangang Yang, Hong Pan, Yanhong Lou and Yuping Zhuge
Plants 2022, 11(14), 1864; https://doi.org/10.3390/plants11141864 - 18 Jul 2022
Cited by 5 | Viewed by 2054
Abstract
Foxtail millet (Setaria italica L.) is an important cereal for managing future water scarcity and ensuring food security, due to its strong drought and salt stress resistance owing to its developed root system. However, the molecular responses of foxtail millet leaves to [...] Read more.
Foxtail millet (Setaria italica L.) is an important cereal for managing future water scarcity and ensuring food security, due to its strong drought and salt stress resistance owing to its developed root system. However, the molecular responses of foxtail millet leaves to salt stress are largely unknown. In this study, seeds of 104 foxtail millet accessions were subjected to 0.17 mol·L−1 NaCl stress during germination, and various germination-related parameters were analyzed to derive 5 salt-sensitive accessions and 13 salt-tolerant accessions. Hong Gu 2000 and Pu Huang Yu were the most salt-tolerant and salt-sensitive accessions, respectively. To determine the mechanism of the salt stress response, transcriptomic differences between the control and salt-treated groups were investigated. We obtained 2019 and 736 differentially expressed genes under salt stress in the salt-sensitive and salt-tolerant accessions, respectively. The transcription factor families bHLH, WRKY, AP2/ERF, and MYB-MYC were found to play critical roles in foxtail millet’s response to salt stress. Additionally, the down-regulation of ribosomal protein-related genes causes stunted growth in the salt-sensitive accessions. The salt-tolerant accession alleviates salt stress by increasing energy production. Our findings provide novel insights into the molecular mechanism of foxtail millet’s response to salt stress. Full article
(This article belongs to the Topic Plant Domestication and Crop Evolution)
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14 pages, 6114 KiB  
Article
Improvements in Sugarcane (Saccharum spp.) Varieties and Parent Traceability Analysis in Yunnan, China
by Yong Zhao, Fenggang Zan, Jun Deng, Peifang Zhao, Jun Zhao, Caiwen Wu, Jiayong Liu and Yuebin Zhang
Agronomy 2022, 12(5), 1211; https://doi.org/10.3390/agronomy12051211 - 18 May 2022
Cited by 4 | Viewed by 2344
Abstract
Sugarcane (Saccharum spp.) breeding in China has a history of nearly 70 years. Yunnan province represents the second largest sugarcane planting area in China; therefore, by studying the evolution of sugarcane varieties in this region, it is possible to gain an understanding [...] Read more.
Sugarcane (Saccharum spp.) breeding in China has a history of nearly 70 years. Yunnan province represents the second largest sugarcane planting area in China; therefore, by studying the evolution of sugarcane varieties in this region, it is possible to gain an understanding of the process of improvement since the foundation of sugarcane hybrid breeding. In this study, we compared the main industrial and agronomical characteristics of 107 sugarcane varieties, developed between 1952 and 2020, and discussed the reasons for replacement and exchange. Overall, significant differences were observed (p < 0.01), highlighting notable improvements, especially in terms of yield; however, disease incidence remains a serious issue and the fundamental reason for variety replacement. Meanwhile, analysis of parent traceability revealed that the main varieties cultivated at present have a similar parental relationship based around CP, F, and YC series germplasms. Taken together, these findings suggest that disease-resistant breeding should be strengthened, and susceptible varieties eliminated, while making full use of existing varieties as core parents. Full article
(This article belongs to the Topic Plant Domestication and Crop Evolution)
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13 pages, 2638 KiB  
Article
The Pid Family Has Been Diverged into Xian and Geng Type Resistance Genes against Rice Blast Disease
by Ruipeng Chai, Jinyan Wang, Xing Wang, Jianqiang Wen, Zhijian Liang, Xuemei Ye, Yaling Zhang, Yongxiang Yao, Jianfu Zhang, Yihua Zhang, Ling Wang and Qinghua Pan
Genes 2022, 13(5), 891; https://doi.org/10.3390/genes13050891 - 17 May 2022
Cited by 1 | Viewed by 1735
Abstract
Rice blast (the causative agent the fungus Magnaporthe oryzae) represents a major constraint on the productivity of one of the world’s most important staple food crops. Genes encoding resistance have been identified in both the Xian and Geng subspecies genepools, and combining [...] Read more.
Rice blast (the causative agent the fungus Magnaporthe oryzae) represents a major constraint on the productivity of one of the world’s most important staple food crops. Genes encoding resistance have been identified in both the Xian and Geng subspecies genepools, and combining these within new cultivars represents a rational means of combating the pathogen. In this research, deeper allele mining was carried out on Pid2, Pid3, and Pid4 via each comprehensive FNP marker set in three panels consisting of 70 Xian and 58 Geng cultivars. Within Pid2, three functional and one non-functional alleles were identified; the former were only identified in Xian type entries. At Pid3, four functional and one non-functional alleles were identified; once again, all of the former were present in Xian type entries. However, the pattern of variation at Pid4 was rather different: here, the five functional alleles uncovered were dispersed across the Geng type germplasm. Among all the twelve candidate functional alleles, both Pid2-ZS and Pid3-ZS were predominant. Furthermore, the resistance functions of both Pid2-ZS and Pid3-ZS were assured by transformation test. Profiting from the merits of three comprehensive FNP marker sets, the study has validated all three members of the Pid family as having been strictly diverged into Xian and Geng subspecies: Pid2 and Pid3 were defined as Xian type resistance genes, and Pid4 as Geng type. Rather limited genotypes of the Pid family have been effective in both Xian and Geng rice groups, of which Pid2-ZS_Pid3-ZS has been central to the Chinese rice population. Full article
(This article belongs to the Topic Plant Domestication and Crop Evolution)
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10 pages, 3599 KiB  
Article
The First Report on Transgenic Hairy Root Induction from the Stem of Tung Tree (Vernicia fordii)
by Hongyu Jia, Junjie Chen, Lin Zhang and Lingling Zhang
Plants 2022, 11(10), 1315; https://doi.org/10.3390/plants11101315 - 16 May 2022
Cited by 5 | Viewed by 2443
Abstract
Tung tree (Vernicia fordii) is an industrially important oil-bearing woody plant of the Euphorbiaceae family. Functional studies of tung tree at the molecular level are limited by the lack of an efficient transgenic system. The Agrobacterium rhizogenes-mediated hairy root generation [...] Read more.
Tung tree (Vernicia fordii) is an industrially important oil-bearing woody plant of the Euphorbiaceae family. Functional studies of tung tree at the molecular level are limited by the lack of an efficient transgenic system. The Agrobacterium rhizogenes-mediated hairy root generation system is an alternative to typical plant transformation systems. However, its application in many plants has been blocked due to the inability of existing methods to induce hairy roots. Thus, it is critical to build a method suitable for the hairy induction of the specific plant of interest. In this study, a modified method for tung tree was developed, and it is the first report that hairy roots could be effectively induced in the stem of tung tree. With the method, an average of 10.7 hairy roots per seedling were generated in tung tree, approximately 67% of seedlings produced transgenic hairy roots and approximately 13.96% of the hairy roots of these seedlings were transgenic. This modified method is also suitable for the hairy root induction of two other oil-bearing plants of the Euphorbiaceae family, Ricinus communis and Vernicia montana. This modified method will accelerate functional studies of tung tree at the molecular level and also shed light on plants lacking a transgenic system. Full article
(This article belongs to the Topic Plant Domestication and Crop Evolution)
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16 pages, 5149 KiB  
Article
Genome-Wide Identification and Evolution Analysis of the Gibberellin Oxidase Gene Family in Six Gramineae Crops
by Chenhao Zhang, Xin Nie, Weilong Kong, Xiaoxiao Deng, Tong Sun, Xuhui Liu and Yangsheng Li
Genes 2022, 13(5), 863; https://doi.org/10.3390/genes13050863 - 12 May 2022
Cited by 10 | Viewed by 2372
Abstract
The plant hormones gibberellins (GAs) regulate plant growth and development and are closely related to the yield of cash crops. The GA oxidases (GAoxs), including the GA2ox, GA3ox, and GA20ox subfamilies, play pivotal roles in GAs’ biosynthesis and metabolism, but their classification and [...] Read more.
The plant hormones gibberellins (GAs) regulate plant growth and development and are closely related to the yield of cash crops. The GA oxidases (GAoxs), including the GA2ox, GA3ox, and GA20ox subfamilies, play pivotal roles in GAs’ biosynthesis and metabolism, but their classification and evolutionary pattern in Gramineae crops remain unclear. We thus conducted a comparative genomic study of GAox genes in six Gramineae representative crops, namely, Setaria italica (Si), Zea mays (Zm), Sorghum bicolor (Sb), Hordeum vulgare (Hv), Brachypodium distachyon (Bd), and Oryza sativa (Os). A total of 105 GAox genes were identified in these six crop genomes, belonging to the C19-GA2ox, C20-GA2ox, GA3ox, and GA20ox subfamilies. Based on orthogroup (OG) analysis, GAox genes were divided into nine OGs and the number of GAox genes in each of the OGs was similar among all tested crops, which indicated that GAox genes may have completed their family differentiations before the species differentiations of the tested species. The motif composition of GAox proteins showed that motifs 1, 2, 4, and 5, forming the 2OG-FeII_Oxy domain, were conserved in all identified GAox protein sequences, while motifs 11, 14, and 15 existed specifically in the GA20ox, C19-GA2ox, and C20-GA2ox protein sequences. Subsequently, the results of gene duplication events suggested that GAox genes mainly expanded in the form of WGD/SD and underwent purification selection and that maize had more GAox genes than other species due to its recent duplication events. The cis-acting elements analysis indicated that GAox genes may respond to growth and development, stress, hormones, and light signals. Moreover, the expression profiles of rice and maize showed that GAox genes were predominantly expressed in the panicles of the above two plants and the expression of several GAox genes was significantly induced by salt or cold stresses. In conclusion, our results provided further insight into GAox genes’ evolutionary differences among six representative Gramineae and highlighted GAox genes that may play a role in abiotic stress. Full article
(This article belongs to the Topic Plant Domestication and Crop Evolution)
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12 pages, 3956 KiB  
Article
Development and Characterization of Chromosome Segment Substitution Lines Derived from Oryza rufipogon in the Background of the Oryza sativa indica Restorer Line R974
by Gumu Ding, Biaolin Hu, Yi Zhou, Wanling Yang, Minmin Zhao, Jiankun Xie and Fantao Zhang
Genes 2022, 13(5), 735; https://doi.org/10.3390/genes13050735 - 22 Apr 2022
Cited by 3 | Viewed by 1829
Abstract
Dongxiang wild rice (DXWR) (O. rufipogon Griff.), which has the northernmost worldwide distribution of a wild rice species, is a valuable genetic resource with respect to improving stress tolerance in cultivated rice (Oryza sativa L.). In the three-line hybrid rice [...] Read more.
Dongxiang wild rice (DXWR) (O. rufipogon Griff.), which has the northernmost worldwide distribution of a wild rice species, is a valuable genetic resource with respect to improving stress tolerance in cultivated rice (Oryza sativa L.). In the three-line hybrid rice breeding system, restorer lines play important roles in enhancing the tolerance of hybrid rice. However, restorer lines have yet to be used as a genomic background for development of substitution lines carrying DXWR chromosome segments. We developed a set of 84 chromosome segment substitution lines (CSSLs) from a donor parent DXWR × recurrent parent restorer line R974 (Oryza sativa indica) cross. On average, each CSSL carried 6.27 introgressed homozygous segments, with 93.37% total genome coverage. Using these CSSLs, we identified a single QTL, qDYST-1, associated with salt stress tolerance on chromosome 3. Furthermore, five CSSLs showing strong salt stress tolerance were subjected to whole-genome single-nucleotide polymorphism chip analyses, during which we detected a common substitution segment containing qDYST-1 in all five CSSLs, thereby implying the validity and efficacy of qDYST-1. These novel CSSLs could make a significant contribution to detecting valuable DXWR QTLs, and provide important germplasm resources for breeding novel restorer lines for use in hybrid rice breeding systems. Full article
(This article belongs to the Topic Plant Domestication and Crop Evolution)
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14 pages, 2608 KiB  
Article
Genetic Diversity and Environmental Influence on Yield and Yield-Related Traits of Adzuki Bean (Vigna angularis L.)
by Liangliang Hu, Gaoling Luo, Xu Zhu, Suhua Wang, Lixia Wang, Xuzhen Cheng and Honglin Chen
Plants 2022, 11(9), 1132; https://doi.org/10.3390/plants11091132 - 21 Apr 2022
Cited by 3 | Viewed by 2108
Abstract
Adzuki beans are an important food legume crop in East Asia. A large number of adzuki bean accessions are maintained in the Chinese national seed genebank. A collection of 59 elite cultivars, 389 landraces, and 27 wild adzuki beans were selected and phenotyped [...] Read more.
Adzuki beans are an important food legume crop in East Asia. A large number of adzuki bean accessions are maintained in the Chinese national seed genebank. A collection of 59 elite cultivars, 389 landraces, and 27 wild adzuki beans were selected and phenotyped extensively for yield and yield-related traits at two different locations (Nanning and Nanyang, China). Ten agronomic and yield-related traits were scored, and the data were subjected to analysis of variance (ANOVA), principal component analysis (PCA), correlation, and cluster analysis. Significant variation was observed for genotypes, locations, and genotype x environment interaction for most traits. Also, there were significant differences in the phenotypes among accessions of different germplasm types. The broad-sense heritability of traits studied ranged from 4.4% to 77.8%. The number of seeds per pod (77.8%), 100-seed weight (68.0%), and number of plant branches (63.9%) had a high heritability. A total of 10 traits were transformed into 3 comprehensive factors by principal component analysis, and the first three principal component factors contributed 72.31% of the total variability. Cluster analysis categorized the 475 adzuki bean accessions into five distinct groups. The results described in this study will be useful for adzuki bean breeders for the development of varieties with high end-use quality. Full article
(This article belongs to the Topic Plant Domestication and Crop Evolution)
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12 pages, 1311 KiB  
Article
Identification and Validation of Reliable Reference Genes for Gene Expression Studies in Koelreuteria paniculata
by Kai Gao, Wasif Ullah Khan, Juan Li, Sai Huang, Xiong Yang, Ting Guo, Bin Guo, Ruqian Wu and Xinmin An
Genes 2022, 13(5), 714; https://doi.org/10.3390/genes13050714 - 19 Apr 2022
Cited by 6 | Viewed by 1731
Abstract
RT-qPCR is considered a rapid and reliable technique for analyzing gene expression. This technique is commonly used to analyze the expression of various genes at diverse transcriptional levels in different samples. However, few studies have characterized ornamental Koelreuteria species for reliable reference genes. [...] Read more.
RT-qPCR is considered a rapid and reliable technique for analyzing gene expression. This technique is commonly used to analyze the expression of various genes at diverse transcriptional levels in different samples. However, few studies have characterized ornamental Koelreuteria species for reliable reference genes. In this study, eight reference genes were evaluated as controls in RT-qPCR with SYBR green to quantify gene expression in different Koelreuteria paniculata samples. All selected reference genes showed a broad range of Ct values in all samples, which was supportive of their variable expression. Our results showed significant variation in the stable expression of K. paniculata genes. Sample data, analyzed using geNorm, NormFinder, and BestKeeper, showed that phospholipase (PLA2) and β-actin (ACT) were the most suitable and statistically reliable reference genes, whereas ribosomal protein L13 (RPL13) and elongation factor 1-α (EF1α) were less stable and unsuitable for use as internal controls. To compare gene expression levels, two or more reference genes should be used for data normalization. Thus, the stability and expression of both PLA2 and ACT were believed to provide better normalization and quantification of the transcript levels for gene expression studies in K. paniculata. Full article
(This article belongs to the Topic Plant Domestication and Crop Evolution)
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