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Pre-breeding towards the Effective Utilization of Plant Genetic Resources

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A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Genetics, Genomics and Biotechnology".

Deadline for manuscript submissions: closed (30 April 2021) | Viewed by 39931

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Dr. Rosalyn B. Angeles-Shim

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Department of Plant and Soil Science, Texas Tech University, 2500 Broadway, Lubbock, TX 79409, USA
Interests: genetic resource development; wide hybridization; molecular breeding; domestication genetics
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Special Issue Information

Dear Colleagues,

There are approximately 300,000 plants species on earth, but only 15 provide 90% of food for human consumption. In the face of continuous agro-environmental decline brought about by climate change, strategies that can maximize the utilization of plant genetic resources will be critical in our collective efforts to develop crops with improved adaptation to temperature extremes, drought, flooding and saline soils, as well as to new biotypes of pests and diseases.

Extensive germplasm collections that include popular cultivars, landraces, and wild relatives of grain, fruit, and vegetable crops have been established in over thousands of genebanks worldwide. In spite of this, utilization of plant genetic resources remains low because of various factors, including the lack of information regarding traits of interest in the germplasm, preference of breeders for working collections, and the challenges associated with the direct use of plant genetic resources in breeding (i.e., reproductive incompatibility and linkage drags).

Pre-breeding is the first key step in utilizing the genetic diversity present in germplasm collections. It encompasses activities designed to identify agronomic traits and/or genes of interest from un-adapted plant materials that cannot be used directly in breeding and introgressing them into an intermediate form of materials that breeders can readily use to produce improved crop varieties.

This Special Issue on “Pre-Breeding toward the Effective Utilization of Plant Genetic Resources” includes papers on both basic and applied research highlighting all aspects of pre-breeding activities from the evaluation of plant genetic resources to identify donors for desirable agronomic traits to the transfer of these target traits into well-adapted genetic backgrounds by hybridizations to generate populations that can be used for actual breeding programs.

Dr. Rosalyn B. Angeles-Shim
Guest Editor

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Keywords

plant genetic resources
wild crop relatives
genetic variation
crop improvement
climate change
adaptation
germplasm
wide hybridization
introgression lines

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Published Papers (12 papers)

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9 pages, 691 KiB

Open AccessCommunication

What Traits Should Be Measured for Biomass in Kenaf?

by Jaeyoung Kim, Gyung Deok Han, Gopi Muthukathan, Renato Rodrogues, Do Yoon Hyun, Seong-Hoon Kim, Ju-Kyung Yu, Jieun Park, Soo-Cheul Yoo and Yong Suk Chung

Plants 2021, 10(7), 1394; https://doi.org/10.3390/plants10071394 - 7 Jul 2021

Cited by 4 | Viewed by 2756

Abstract

Kenaf (Hibiscus cannabinus L.) is widely used as an important industrial crop. It has the potential to act as a sustainable energy provider in the future, and contains beneficial compounds for medical and therapeutic use. However, there are no clear breeding strategies to increase its biomass or leaf volume. Thus, to attain an increase in these parameters, we examined potential key traits such as stem diameter, plant height, and number of nodes to determine the relationship among them. We hypothesized that it would be easier to reduce the amount of time and labor required for breeding if correlations among these parameters are identified. In this study, we found a strong positive correlation between height and number of nodes (Spearman’s Rho = 0.67, p < 0.001) and number of nodes and stem diameter (Spearman’s Rho = 0.65, p < 0.001), but a relatively low correlation (Spearman’s Rho = 0.34, p < 0.01) between height and stem diameter in the later stages of kenaf growth. We suggest that an efficient breeding strategy could be devised according to the breeding purpose, considering the correlations between various individual traits of kenaf. Full article

(This article belongs to the Special Issue Pre-breeding towards the Effective Utilization of Plant Genetic Resources)

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14 pages, 4207 KiB

Open AccessArticle

ISSR-Based Genetic Diversity Assessment of Genus Jasminum L. (Oleaceae) from Pakistan

by Naeem Akhtar, Ishfaq Ahmad Hafiz, Muhammad Qasim Hayat, Daniel Potter, Nadeem Akhtar Abbasi, Umer Habib, Adil Hussain, Hina Hafeez, Muhammad Ajmal Bashir and Saad Imran Malik

Plants 2021, 10(7), 1270; https://doi.org/10.3390/plants10071270 - 22 Jun 2021

Cited by 11 | Viewed by 3544

Abstract

The genus Jasminum L., of the family Oleaceae, includes many species occurring in the wild, or cultivated worldwide. A preliminary investigation based on inter-simple sequence repeats (ISSR) was performed to assess the genetic diversity among 28 accessions, representing nine species of Jasminum from various regions, representing a range of altitudes in Pakistan. A total of 21 ISSR primers were used, which produced 570 amplified bands of different sizes, with a mean polymorphic band percentage of 98.26%. The maximum resolving power, polymorphism information content, and index values of the ISSR markers recorded for primers 6, 16, and 19 were 0.40, 12.32, and 24.21, respectively. Based on the data of the ISSR markers, the resulting UPGMA dendrogram with the Jaccard coefficient divided the 28 accessions into two main clades. At the species level, the highest values for Shannon’s information index, polymorphism percentage, effective allele number, Nei’s genetic variations, and genetic unbiased diversity were found in Jasminum sambac L. and J. humile L., while the lowest were observed in J. mesnyi Hance and J. nitidum Skan. Based on Nei’s unbiased genetic identity pairwise population matrix, the maximum identity (0.804) was observed between J. elongatum Willd and J. multiflorum (Burm. f.) Andrews, and the lowest (0.566) between J. nitidum Skan. and J. azoricum L. Molecular variance analysis displayed a genetic variation of 79% among the nine populations. The study was aimed to established genetic diversity in Jasminum species using ISSR markers. With the help of this technique, we were able to establish immense intra- and interspecific diversity across the Jasminum species. Full article

(This article belongs to the Special Issue Pre-breeding towards the Effective Utilization of Plant Genetic Resources)

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16 pages, 560 KiB

Open AccessArticle

Evaluation of Scab and Mildew Resistance in the Gene Bank Collection of Apples in Dresden-Pillnitz

by Monika Höfer, Henryk Flachowsky, Susan Schröpfer and Andreas Peil

Plants 2021, 10(6), 1227; https://doi.org/10.3390/plants10061227 - 16 Jun 2021

Cited by 27 | Viewed by 3197

Abstract

A set of 680 apple cultivars from the Fruit Gene bank in Dresden Pillnitz was evaluated for the incidence of powdery mildew and scab in two consecutive years. The incidence of both scab and powdery mildew increased significantly in the second year. Sixty and 43 cultivars with very low incidence in both years of scab and powdery mildew, respectively, were analysed with molecular markers linked to known resistance genes. Thirty-five cultivars were identified to express alleles or combinations of alleles linked to Rvi2, Rvi4, Rvi6, Rvi13, Rvi14, or Rvi17. Twenty of them, modern as well as a few traditional cultivars known before the introduction or Rvi6 from Malus floribunda 821, amplified the 159 bp fragment of marker CH_Vf1 that is linked to Rvi6. Alleles linked to Pl1, Pld, or Plm were expressed from five cultivars resistant to powdery mildew. Eleven cultivars were identified to have very low susceptibility to both powdery mildew and scab. The information on resistance/susceptibility of fruit genetic resources towards economically important diseases is important for breeding and for replanting traditional cultivars. Furthermore, our work provides a well-defined basis for the discovery of undescribed, new scab, and powdery mildew resistance. Full article

(This article belongs to the Special Issue Pre-breeding towards the Effective Utilization of Plant Genetic Resources)

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13 pages, 3024 KiB

Open AccessArticle

Genome-Wide Association Analysis for Stem Cross Section Properties, Height and Heading Date in a Collection of Spanish Durum Wheat Landraces

by Carmen M. Ávila, María Dolores Requena-Ramírez, Cristina Rodríguez-Suárez, Fernando Flores, Josefina C. Sillero and Sergio G. Atienza

Plants 2021, 10(6), 1123; https://doi.org/10.3390/plants10061123 - 1 Jun 2021

Cited by 10 | Viewed by 3304

Abstract

Durum wheat landraces have a high potential for breeding but they remain underexploited due to several factors, including the insufficient evaluation of these plant materials and the lack of efficient selection tools for transferring target traits into elite backgrounds. In this work, we characterized 150 accessions of the Spanish durum wheat collection for stem cross section, height and heading date. Continuous variation and high heritabilities were recorded for the stem area, pith area, pith diameter, culm wall thickness, height and heading date. The accessions were genotyped with DArTSeq markers, which were aligned to the durum wheat ‘Svevo’ genome. The markers corresponding to genes, with a minor allele frequency above 5% and less than 10% of missing data, were used for genome-wide association scan analysis. Twenty-nine marker-trait associations (MTAs) were identified and compared with the positions of previously known QTLs. MTAs for height and heading date co-localized with the QTLs for these traits. In addition, all the MTAs for stem traits in chromosome 2B were located in the corresponding synteny regions of the markers associated with lodging in bread wheat. Finally, several MTAs for stem traits co-located with the QTL for wheat stem sawfly (WSS) resistance. The results presented herein reveal the same genomic regions in chromosome 2B are involved in the genetic control of stem traits and lodging tolerance in both durum and bread wheat. In addition, these results suggest the importance of stem traits for WSS resistance and the potential of these landraces as donors for lodging tolerance and WSS resistance enhancement. In this context, the MTAs for stem-related traits identified in this work can serve as a reference for further development of markers for the introgression of target traits into elite material. Full article

(This article belongs to the Special Issue Pre-breeding towards the Effective Utilization of Plant Genetic Resources)

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15 pages, 3485 KiB

Open AccessArticle

Genome-Wide Identification and Development of LTR Retrotransposon-Based Molecular Markers for the Melilotus Genus

by Zifeng Ouyang, Yimeng Wang, Tiantian Ma, Gisele Kanzana, Fan Wu and Jiyu Zhang

Plants 2021, 10(5), 890; https://doi.org/10.3390/plants10050890 - 28 Apr 2021

Cited by 9 | Viewed by 2232

Abstract

Melilotus is an important genus of legumes with industrial and medicinal value, partly due to the production of coumarin. To explore the genetic diversity and population structure of Melilotus, 40 accessions were analyzed using long terminal repeat (LTR) retrotransposon-based markers. A total of 585,894,349 bp of LTR retrotransposon sequences, accounting for 55.28% of the Melilotus genome, were identified using bioinformatics tools. A total of 181,040 LTR retrotransposons were identified and classified as Gypsy, Copia, or another type. A total of 350 pairs of primers were designed for assessing polymorphisms in 15 Melilotus albus accessions. Overall, 47 polymorphic primer pairs were screened for their availability and transferability in 18 Melilotus species. All the primer pairs were transferable, and 292 alleles were detected at 47 LTR retrotransposon loci. The average polymorphism information content (PIC) value was 0.66, which indicated that these markers were highly informative. Based on unweighted pair group method with arithmetic mean (UPGMA) dendrogram cluster analysis, the 18 Melilotus species were classified into three clusters. This study provides important data for future breeding programs and for implementing genetic improvements in the Melilotus genus. Full article

(This article belongs to the Special Issue Pre-breeding towards the Effective Utilization of Plant Genetic Resources)

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22 pages, 866 KiB

Open AccessArticle

Evaluation and Selection of Interspecific Lines of Groundnut (Arachis hypogaea L.) for Resistance to Leaf Spot Disease and for Yield Improvement

by Nicholas N. Denwar, Charles E. Simpson, James L. Starr, Terry A. Wheeler and Mark D. Burow

Plants 2021, 10(5), 873; https://doi.org/10.3390/plants10050873 - 26 Apr 2021

Cited by 13 | Viewed by 3086

Abstract

Early and late leaf spot are two devastating diseases of peanut (Arachis hypogaea L.) worldwide. The development of a fertile, cross-compatible synthetic amphidiploid, TxAG-6 ([A. batizocoi × (A. cardenasii × A. diogoi)]^4x), opened novel opportunities for the introgression of wild alleles for disease and pest resistance into commercial cultivars. Twenty-seven interspecific lines selected from prior evaluation of an advanced backcross population were evaluated for resistance to early and late leaf spot, and for yield in two locations in Ghana in 2006 and 2007. Several interspecific lines had early leaf spot scores significantly lower than the susceptible parent, indicating that resistance to leaf spot had been successfully introgressed and retained after three cycles of backcrossing. Time to appearance of early leaf spot symptoms was less in the introgression lines than in susceptible check cultivars, but the opposite was true for late leaf spot. Selected lines from families 43-08, 43-09, 50-04, and 60-02 had significantly reduced leaf spot scores, while lines from families 43-09, 44-10, and 63-06 had high pod yields. One line combined both resistance to leaf spot and high pod yield, and several other useful lines were also identified. Results suggest that it is possible to break linkage drag for low yield that accompanies resistance. However, results also suggest that resistance was diluted in many of the breeding lines, likely a result of the multigenic nature of resistance. Future QTL analysis may be useful to identify alleles for resistance and allow recombination and pyramiding of resistance alleles while reducing linkage drag. Full article

(This article belongs to the Special Issue Pre-breeding towards the Effective Utilization of Plant Genetic Resources)

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16 pages, 1674 KiB

Open AccessArticle

Phenotypic Diversity and Productivity of Medicago sativa Subspecies from Drought-Prone Environments in Mediterranean Type Climates

by Luis Inostroza, Soledad Espinoza, Viviana Barahona, Macarena Gerding, Alan Humphries, Alejandro del Pozo and Carlos Ovalle

Plants 2021, 10(5), 862; https://doi.org/10.3390/plants10050862 - 24 Apr 2021

Cited by 9 | Viewed by 2701

Abstract

The phenotypic diversity and productivity of a diverse alfalfa (M. sativa subspp.) panel of cultivars, landraces and wild relatives with putative drought tolerance were evaluated in two Mediterranean environments (central Chile and Southern Australia). In Chile, 70 accessions were evaluated in rainfed conditions and in Australia 30 accessions under rainfed and irrigated conditions, during three growing seasons. Large phenotypic variation was observed among and within subspecies for NDVI, stem length, intercepted PAR and forage yield. Principal component analysis indicated that the first two principal components (PC) accounted for 84.2% of total variance; fall dormancy, taxa, and breeding status were closely related to the agronomical performance of alfalfa accessions. Forage yield varied largely among accessions across years and locations. A linear relationship was found between annual forage yield and annual water added to the experiments (R² = 0.60, p < 0.001). The GxE analysis for forage yield allowed the detection of the highest yielding accessions for each of the two mega-environments identified. The accessions CTA002 and CTA003 showed greater forage yield in both Chile and Australia environments. It is concluded that new breeding lines derived from crosses between cultivated alfalfa (M. sativa subsp. sativa) and wild relatives belonging to the primary (M. sativa subsp. falcata) and tertiary (M. arborea) gene pool, achieve outstanding agronomical performance in drought-prone environments. Full article

(This article belongs to the Special Issue Pre-breeding towards the Effective Utilization of Plant Genetic Resources)

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18 pages, 1786 KiB

Open AccessArticle

Exploring the Loci Responsible for Awn Development in Rice through Comparative Analysis of All AA Genome Species

by Kanako Bessho-Uehara, Yoshiyuki Yamagata, Tomonori Takashi, Takashi Makino, Hideshi Yasui, Atsushi Yoshimura and Motoyuki Ashikari

Plants 2021, 10(4), 725; https://doi.org/10.3390/plants10040725 - 8 Apr 2021

Cited by 9 | Viewed by 3483

Abstract

Wild rice species have long awns at their seed tips, but this trait has been lost through rice domestication. Awn loss mitigates harvest and seed storage; further, awnlessness increases the grain number and, subsequently, improves grain yield in Asian cultivated rice, highlighting the contribution of the loss of awn to modern rice agriculture. Therefore, identifying the genes regulating awn development would facilitate the elucidation of a part of the domestication process in rice and increase our understanding of the complex mechanism in awn morphogenesis. To identify the novel loci regulating awn development and understand the conservation of genes in other wild rice relatives belonging to the AA genome group, we analyzed the chromosome segment substitution lines (CSSL). In this study, we compared a number of CSSL sets derived by crossing wild rice species in the AA genome group with the cultivated species Oryza sativa ssp. japonica. Two loci on chromosomes 7 and 11 were newly discovered to be responsible for awn development. We also found wild relatives that were used as donor parents of the CSSLs carrying the functional alleles responsible for awn elongation, REGULATOR OF AWN ELONGATION 1 (RAE1) and RAE2. To understand the conserveness of RAE1 and RAE2 in wild rice relatives, we analyzed RAE1 and RAE2 sequences of 175 accessions among diverse AA genome species retrieved from the sequence read archive (SRA) database. Comparative sequence analysis demonstrated that most wild rice AA genome species maintained functional RAE1 and RAE2, whereas most Asian rice cultivars have lost either or both functions. In addition, some different loss-of-function alleles of RAE1 and RAE2 were found in Asian cultivated species. These findings suggest that different combinations of dysfunctional alleles of RAE1 and RAE2 were selected after the speciation of O. sativa, and that two-step loss of function in RAE1 and RAE2 contributed to awnlessness in Asian cultivated rice. Full article

(This article belongs to the Special Issue Pre-breeding towards the Effective Utilization of Plant Genetic Resources)

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16 pages, 3499 KiB

Open AccessArticle

Small “Nested” Introgressions from Wild Thinopyrum Species, Conferring Effective Resistance to Fusarium Diseases, Positively Impact Durum Wheat Yield Potential

by Ljiljana Kuzmanović, Gloria Giovenali, Roberto Ruggeri, Francesco Rossini and Carla Ceoloni

Plants 2021, 10(3), 579; https://doi.org/10.3390/plants10030579 - 19 Mar 2021

Cited by 9 | Viewed by 2584

Abstract

Today wheat cultivation is facing rapidly changing climate scenarios and yield instability, aggravated by the spreading of severe diseases such as Fusarium head blight (FHB) and Fusarium crown rot (FCR). To obtain productive genotypes resilient to stress pressure, smart breeding approaches must be envisaged, including the exploitation of wild relatives. Here we report on the assessment of the breeding potential of six durum wheat-Thinopyrum spp. recombinant lines (RLs) obtained through chromosome engineering. They are characterized by having 23% or 28% of their 7AL chromosome arm replaced by a “nested” alien segment, composed of homoeologous group 7 chromosome fractions from Th. ponticum and Th. elongatum (=7el₁L + 7EL) or from different Th. ponticum accessions (=7el₁L + 7el₂L). In addition to the 7el₁L genes Lr19 + Yp (leaf rust resistance, and yellow pigment content, respectively), these recombinant lines (RLs) possess a highly effective QTL for resistance to FHB and FCR within their 7el₂L or 7EL portion. The RLs, their null segregants and well-adapted and productive durum wheat cultivars were evaluated for 16 yield-related traits over two seasons under rainfed and irrigated conditions. The absence of yield penalties and excellent genetic stability of RLs was revealed in the presence of all the alien segment combinations. Both 7el₂L and 7EL stacked introgressions had positive impacts on source and sink yield traits, as well as on the overall performance of RLs in conditions of reduced water availability. The four “nested” RLs tested in 2020 were among the top five yielders, overall representing good candidates to be employed in breeding programs to enhance crop security and safety. Full article

(This article belongs to the Special Issue Pre-breeding towards the Effective Utilization of Plant Genetic Resources)

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14 pages, 4078 KiB

Open AccessArticle

Population Structure and Genetic Diversity in Korean Cowpea Germplasm Based on SNP Markers

by Eunju Seo, Kipoong Kim, Tae-Hwan Jun, Jinsil Choi, Seong-Hoon Kim, María Muñoz-Amatriaín, Hokeun Sun and Bo-Keun Ha

Plants 2020, 9(9), 1190; https://doi.org/10.3390/plants9091190 - 12 Sep 2020

Cited by 18 | Viewed by 4306

Abstract

Cowpea is one of the most essential legume crops providing inexpensive dietary protein and nutrients. The aim of this study was to understand the genetic diversity and population structure of global and Korean cowpea germplasms. A total of 384 cowpea accessions from 21 countries were genotyped with the Cowpea iSelect Consortium Array containing 51,128 single-nucleotide polymorphisms (SNPs). After SNP filtering, a genetic diversity study was carried out using 35,116 SNPs within 376 cowpea accessions, including 229 Korean accessions. Based on structure and principal component analysis, a total of 376 global accessions were divided into four major populations. Accessions in group 1 were from Asia and Europe, those in groups 2 and 4 were from Korea, and those in group 3 were from West Africa. In addition, 229 Korean accessions were divided into three major populations (Q1, Jeonra province; Q2, Gangwon province; Q3, a mixture of provinces). Additionally, the neighbor-joining tree indicated similar results. Further genetic diversity analysis within the global and Korean population groups indicated low heterozygosity, a low polymorphism information content, and a high inbreeding coefficient in the Korean cowpea accessions. The population structure analysis will provide useful knowledge to support the genetic potential of the cowpea breeding program, especially in Korea. Full article

(This article belongs to the Special Issue Pre-breeding towards the Effective Utilization of Plant Genetic Resources)

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14 pages, 2512 KiB

Open AccessFeature PaperReview

Finding Needles in a Haystack: Using Geo-References to Enhance the Selection and Utilization of Landraces in Breeding for Climate-Resilient Cultivars of Upland Cotton (Gossypium hirsutum L.)

by Junghyun Shim, Nonoy B. Bandillo and Rosalyn B. Angeles-Shim

Plants 2021, 10(7), 1300; https://doi.org/10.3390/plants10071300 - 26 Jun 2021

Cited by 5 | Viewed by 3251

Abstract

The genetic uniformity of cultivated cotton as a consequence of domestication and modern breeding makes it extremely vulnerable to abiotic challenges brought about by major climate shifts. To sustain productivity amidst worsening agro-environments, future breeding objectives need to seriously consider introducing new genetic variation from diverse resources into the current germplasm base of cotton. Landraces are genetically heterogeneous, population complexes that have been primarily selected for their adaptability to specific localized or regional environments. This makes them an invaluable genetic resource of novel allelic diversity that can be exploited to enhance the resilience of crops to marginal environments. The utilization of cotton landraces in breeding programs are constrained by the phenology of the plant and the lack of phenotypic information that can facilitate efficient selection of potential donor parents for breeding. In this review, the genetic value of cotton landraces and the major challenges in their utilization in breeding are discussed. Two strategies namely Focused Identification of Germplasm Strategy and Environmental Association Analysis that have been developed to effectively screen large germplasm collections for accessions with adaptive traits using geo-reference-based, mathematical modelling are highlighted. The potential applications of both approaches in mining available cotton landrace collections are also presented. Full article

(This article belongs to the Special Issue Pre-breeding towards the Effective Utilization of Plant Genetic Resources)

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12 pages, 294 KiB

Open AccessReview

Tritordeum: Creating a New Crop Species—The Successful Use of Plant Genetic Resources

by Carmen M. Ávila, Cristina Rodríguez-Suárez and Sergio G. Atienza

Plants 2021, 10(5), 1029; https://doi.org/10.3390/plants10051029 - 20 May 2021

Cited by 24 | Viewed by 3570

Abstract

Hexaploid tritordeum is the amphiploid derived from the cross between the wild barley Hordeum chilense and durum wheat. This paper reviews the main advances and achievements in the last two decades that led to the successful development of tritordeum as a new crop. In particular, we summarize the progress in breeding for agronomic performance, including the potential of tritordeum as a genetic bridge for wheat breeding; the impact of molecular markers in genetic studies and breeding; and the progress in quality and development of innovative food products. The success of tritordeum as a crop shows the importance of the effective utilization of plant genetic resources for the development of new innovative products for agriculture and industry. Considering that wild plant genetic resources have made possible the development of this new crop, the huge potential of more accessible resources, such as landraces conserved in gene banks, goes beyond being sources of resistance to biotic and abiotic stresses. In addition, the positive result of tritordeum also shows the importance of adequate commercialization strategies and demonstrative experiences aimed to integrate the whole food chain, from producers to end-point sellers, in order to develop new products for consumers. Full article

(This article belongs to the Special Issue Pre-breeding towards the Effective Utilization of Plant Genetic Resources)

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