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Genetic Associated Plant Breeding
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Genetic Associated Plant Breeding

A special issue of Life (ISSN 2075-1729). This special issue belongs to the section "Plant Science".

Deadline for manuscript submissions: closed (31 December 2023) | Viewed by 10869

Special Issue Editors

Dr. Shivali Sharma

E-Mail Website
Guest Editor
Global Crop Diversity Trust, Bonn, Germany
Interests: plant genetic resources conservation and utilization; crop wild relatives; plant breeding; genetics; pre-breeding; tissue culture; doubled-haploidy breeding
Dr. Pooran Gaur

E-Mail Website
Guest Editor
The UWA Institute of Agriculture, The University of Western Australia, Perth, Australia
Interests: genetics and breeding of food legumes; application of novel tools and techniques in breeding; seed system

Special Issue Information

Dear Colleagues,

The application of genetics in developing improved crop varieties has played a pivotal role in improving agricultural food production. The efficiency of plant breeding has continued to improve over the years through increased understanding of the genetics of traits and use of genetics-based breeding strategies. The recent advances in the development and application of modern tools and technologies, such as genomic selection, genome editing and speed breeding, have further enhanced the precision and efficiency of plant breeding and presented tremendous opportunities to achieve rapid genetic gains. This is important for the rapid development of improved varieties which are high yielding, nutritionally rich and climate-resilient, and have other traits preferred by farmers, consumers and industries.

This Special Issue focuses on publishing original research, reviews and opinion articles highlighting basic, strategic and applied research in the field of genetics, genomics and plant breeding. The topics include, but are not limited to: the recent advances in genomics and trait discovery, identification and exploitation of novel alleles from the plant genetic resources including crop wild relatives, trait deployment for developing new improved varieties, and genetic engineering and genome editing for targeted breeding of food crops.  

Dr. Shivali Sharma
Dr. Pooran Gaur
Guest Editors

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Keywords

  • genetics
  • genebanks
  • plant breeding
  • plant genetic resources
  • crop wild relatives
  • pre-breeding
  • genetic engineering
  • genomics
  • genome editing
  • rait deployment
  • speed breeding
  • marker-assisted selection

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Published Papers (5 papers)

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Research

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13 pages, 1663 KiB  
Article
Genetic Analysis of Adaptive Traits in Spring Wheat in Northeast China
by Hongji Zhang, Yuyao Li, Wenlin Liu, Yan Sun, Jingquan Tang, Jingyu Che, Shuping Yang, Xiangyu Wang and Rui Zhang
Life 2024, 14(2), 168; https://doi.org/10.3390/life14020168 - 24 Jan 2024
Viewed by 1328
Abstract
The dissection of the genetic architecture and the detection of the loci for adaptive traits are important for marker-assisted selection (MAS) for breeding. A spring wheat diversity panel with 251 cultivars, mainly from China, was obtained to conduct a genome-wide association study (GWAS) [...] Read more.
The dissection of the genetic architecture and the detection of the loci for adaptive traits are important for marker-assisted selection (MAS) for breeding. A spring wheat diversity panel with 251 cultivars, mainly from China, was obtained to conduct a genome-wide association study (GWAS) to detect the new loci, including the heading date (HD), maturating date (MD), plant height (PH), and lodging resistance (LR). In total, 41 loci existing in all 21 chromosomes, except for 4A and 6B, were identified, and each explained 4.3–18.9% of the phenotypic variations existing in two or more environments. Of these, 13 loci are overlapped with the known genes or quantitative trait loci (QTLs), whereas the other 28 are likely to be novel. The 1A locus (296.9–297.7 Mb) is a multi-effect locus for LR and PH, whereas the locus on chromosome 6D (464.5–471.0 Mb) affects both the HD and MD. Furthermore, four candidate genes for adaptive traits were identified, involved in cell division, signal transduction, and plant development. Additionally, two competitive, allele-specific PCR (KASP) markers, Kasp_2D_PH for PH and Kasp_6D_HD for HD, were developed and validated in another 162 spring wheat accessions. Our study uncovered the genetic basis of adaptive traits and provided the associated SNPs and varieties with more favorable alleles for wheat MAS breeding. Full article
(This article belongs to the Special Issue Genetic Associated Plant Breeding)
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14 pages, 1496 KiB  
Article
The Fastest and Most Reliable Identification of True Hybrids in the Genus Pisum L.
by Hatice Sari, Tuba Eker, Duygu Sari, Munevver Aksoy, Melike Bakır, Veysel Dogdu, Cengiz Toker and Huseyin Canci
Life 2023, 13(11), 2222; https://doi.org/10.3390/life13112222 - 18 Nov 2023
Cited by 2 | Viewed by 1342
Abstract
After crosses, the identification of true hybrids is not only the most important step in the initiation of a breeding program but also plays a crucial role in the improvement of hybrid varieties. However, current morphological or molecular-based hybrid identification methods are time-consuming [...] Read more.
After crosses, the identification of true hybrids is not only the most important step in the initiation of a breeding program but also plays a crucial role in the improvement of hybrid varieties. However, current morphological or molecular-based hybrid identification methods are time-consuming and costly approaches that require knowledge and skill, as well as specific lab equipment. In the current study, xenia, direct or immediate effect of pollen on seeds was used to identify true hybrids in the genus Pisum L. for the first time without growing F1 plants. The current study was therefore aimed to (i) elucidate the xenia effect on seeds in intra- and interspecific crosses between P. sativum L. subsp. sativum var. sativum or var. arvense L. Poir. and its wild relatives, including P. sativum subsp. elatius (M. Bieb.) Aschers & Graebn. and P. fulvum Sibth. & Sm., and (ii) illuminate the beneficialness of the xenia effect in a practical improvement of the genus Pisum L. The pea cultivars, including P. sativum subsp. sativum var. sativum and P. sativum subsp. sativum var. arvense, were therefore crossed with P. sativum subsp. elatius and P. fulvum, and the occurrence of the xenia effect was studied on the seeds of fertilized female plants immediately after the crosses. It was concluded that using the xenia effect for the early detection of true hybrid immediately after crossing was not only the fastest, most reliable, and least expensive option as early selection criteria, but that xenia also provided information about dominant seed and pod traits after double fertilization. Full article
(This article belongs to the Special Issue Genetic Associated Plant Breeding)
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13 pages, 1932 KiB  
Article
Next-Generation-Sequencing-Based Simple Sequence Repeat (SSR) Marker Development and Linkage Mapping in Lentil (Lens culinaris L.)
by Mustafa Topu, Uğur Sesiz, Harun Bektaş, Faruk Toklu and Hakan Özkan
Life 2023, 13(7), 1579; https://doi.org/10.3390/life13071579 - 18 Jul 2023
Cited by 3 | Viewed by 2320
Abstract
Simple sequence repeats (SSRs) are highly versatile markers in genetic diversity analysis and plant breeding, making them widely applicable. They hold potential in lentil (Lens culinaris) breeding for genetic diversity analysis, marker-assisted selection (MAS), and linkage mapping. However, the availability and [...] Read more.
Simple sequence repeats (SSRs) are highly versatile markers in genetic diversity analysis and plant breeding, making them widely applicable. They hold potential in lentil (Lens culinaris) breeding for genetic diversity analysis, marker-assisted selection (MAS), and linkage mapping. However, the availability and diversity of SSR markers in lentil is limited. We used next-generation sequencing (NGS) technology to develop SSR markers in lentil. NGS allowed us to identify regions of the lentil genome that contained SSRs. Illumina Hiseq-2000 sequencing of the lentil genotype “Karacadağ” resulted in 1,727,734 sequence reads comprising more than 48,390 Mb, and contigs were mined for SSRs, resulting in the identification of a total of 8697 SSR motifs. Among these, dinucleotide repeats were the most abundant (53.38%), followed by trinucleotides (30.38%), hexanucleotides (6.96%), tetranucleotides (6.59%), and pentanucleotides (3.19%). The most frequent repeat in dinucleotides was the TC (21.80%), followed by the GA (17.60%). A total of 2000 primer pairs were designed from these motifs, and 458 SSR markers were validated following their amplified PCR products. A linkage map was constructed using these new SSRs with high linkage disequilibrium (209) and previously known SSRs (11). The highest number of SSR markers (43) was obtained in LG2, while the lowest number of SSR markers (19) was obtained in LG7. The longest linkage group (LG) was LG2 (86.84 cM), whereas the shortest linkage group was LG7 (53.46 cM). The average length between markers ranged from 1.86 cM in LG1 to 2.81 cM in LG7, and the map density was 2.16 cM. The developed SSRs and created linkage map may provide useful information and offer a new library for genetic diversity analyses, linkage mapping studies, and lentil breeding programs. Full article
(This article belongs to the Special Issue Genetic Associated Plant Breeding)
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22 pages, 4048 KiB  
Article
Selection and Molecular Characterization of Promising Plum Rootstocks (Prunus cerasifera L.) among Seedling-Origin Trees
by Kubra Korkmaz, Ibrahim Bolat, Aydın Uzun, Muge Sahin and Ozkan Kaya
Life 2023, 13(7), 1476; https://doi.org/10.3390/life13071476 - 29 Jun 2023
Cited by 4 | Viewed by 2084
Abstract
The plum (Prunus cerasifera Ehrh) has been used worldwide both as a genetic source for breeding new rootstocks and as clonal rootstock for many Prunus species. Considering situations where wild relatives of plums are endangered, in-depth characterization of rootstock traits of genetic [...] Read more.
The plum (Prunus cerasifera Ehrh) has been used worldwide both as a genetic source for breeding new rootstocks and as clonal rootstock for many Prunus species. Considering situations where wild relatives of plums are endangered, in-depth characterization of rootstock traits of genetic diversity of plum germplasm of Turkey with many ecogeographical locations is crucial. In the present study, therefore, three steps were followed for the selection of rootstock candidates among the plum germplasm grown in the Middle Euphrates. This region is characterized by an extremely hot climate with extremely warm summers and very low precipitation in summers. Initially, 79 rootstock candidates were selected based on rootstocks traits, and Myrobalan 29C was also used for the control rootstock in all steps. Hardwood cuttings were taken from each rootstock candidate, and after the rooting process in rootstock candidates, 39 rootstock candidates outperforming other candidates were selected according to root characteristics. Based on rooting ability, forty rootstock candidates with the longest root length below 33.50 mm, root number below 3.00, and rooting cutting number below 30.00% were eliminated. The second step of the study focused on the dwarfing characteristics of 39 rootstock candidates, and 13 and Myrobalan 29C out of 39 rootstock candidates’ dwarfing traits showed value higher compared to the other 26 rootstock candidates. Results indicated that the vigor of rootstock candidates was usually found to be strong (26), intermediate (4), and weak (9). Moreover, 13 out of 39 rootstock candidates’ dwarfism trait was better than the other 26 rootstock candidates. In Step 3, some morphological, physiological, and molecular evaluations were conducted in 13 rootstock candidates and the Myrobalan 29C clone, and there were significant differences between both rootstock candidates and the parameters evaluated. PCA has also been indicated that the reference rootstock Myrobalan 29C was grouped with 63B62, 63B69, and 63B14. The highest genetic similarity was found between 63B11 and 63B16, as well as between 63B76 and 63B66, while the lowest genetic similarity was observed between 63B72 and 63B61 candidates. Overall, the findings presented here provide valuable information about the level of rootstock candidates that could potentially be superior among previously uncharacterized plum cultivars in this plum-growing region of Turkey. Full article
(This article belongs to the Special Issue Genetic Associated Plant Breeding)
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Review

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28 pages, 2875 KiB  
Review
The Progression in Developing Genomic Resources for Crop Improvement
by Pradeep Ruperao, Parimalan Rangan, Trushar Shah, Vivek Thakur, Sanjay Kalia, Sean Mayes and Abhishek Rathore
Life 2023, 13(8), 1668; https://doi.org/10.3390/life13081668 - 31 Jul 2023
Viewed by 2496
Abstract
Sequencing technologies have rapidly evolved over the past two decades, and new technologies are being continually developed and commercialized. The emerging sequencing technologies target generating more data with fewer inputs and at lower costs. This has also translated to an increase in the [...] Read more.
Sequencing technologies have rapidly evolved over the past two decades, and new technologies are being continually developed and commercialized. The emerging sequencing technologies target generating more data with fewer inputs and at lower costs. This has also translated to an increase in the number and type of corresponding applications in genomics besides enhanced computational capacities (both hardware and software). Alongside the evolving DNA sequencing landscape, bioinformatics research teams have also evolved to accommodate the increasingly demanding techniques used to combine and interpret data, leading to many researchers moving from the lab to the computer. The rich history of DNA sequencing has paved the way for new insights and the development of new analysis methods. Understanding and learning from past technologies can help with the progress of future applications. This review focuses on the evolution of sequencing technologies, their significant enabling role in generating plant genome assemblies and downstream applications, and the parallel development of bioinformatics tools and skills, filling the gap in data analysis techniques. Full article
(This article belongs to the Special Issue Genetic Associated Plant Breeding)
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