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Genetic Diversity Assessment and Marker-Assisted Selection in Crops

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A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Plant Genetics and Genomics".

Deadline for manuscript submissions: closed (10 May 2020) | Viewed by 39413

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Special Issue Editors

Dr. Francesco Mercati

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Guest Editor

Institute of Biosciences and BioResources, Division of Palermo, National Research Council, Corso Calatafimi, 414, I-90129 Palermo, Italy
Interests: plant genetics; plant nutrition; breeding; molecular markers; NGS (next-generation sequencing); PGPR
Special Issues, Collections and Topics in MDPI journals

Dr. Francesco Sunseri

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Department AGRARIA, University Mediterranea of Reggio Calabria, Località Feo di Vito snc, I-89124 Reggio Calabria, Italy
Interests: plant genetics and breeding; molecular-assisted selection (MAS); vegetable crops (mainly tomato and eggplant); abiotic stress; nitrogen use efficiency (NUE); genetic structure of plant biodiversity; genomics; transcriptomics; genotyping-by-sequencing (GBS)
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Global warming is changing Earth's climate with possible negative effects on the growth and reproductive success of crops. Reduced plant productivity due to environmental changes might implicate ineffectiveness to ensure global food security. Therefore, the exploitation of biodiversity is needed to select more resilient genotypes/crops employable in more sustainable cropping systems. Different approaches can be followed, through both the selection and introduction of stress-tolerant cultivars of existing crops, but also by genes/QTLs introgression from interspecific crosses between cultivated and wild species and promoting alternative crop species, such as “orphan” crops.

The estimation of genetic diversity and the selection of genomic regions mapping traits of interest are two pivotal points for future breeding programs.

The advent of next-generation sequencing (NGS) technologies allowed us to easily re-sequence the whole genome to develop high-density genotyping arrays for many plants. The genomic variants identification, such as single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) markers, together with high throughput phenotyping, supported the genome-wide association studies (GWAS) and genomic selection (GS) in crops, two powerful tools useful for highlighting the genome-to-phenome relationship. These technologies have allowed disruptive improvements in breeding strategies that can be rapidly applied to select new resilient genotypes in many crops, mainly vegetables. The different approaches encourage the selection of superior genotypes, reducing the breeding cycle in a cost-effective manner.

This Special Issue will focus on the development and application of such technologies associated with adaptation and functional crop improvement, exploiting the available biodiversity in crops.

Dr. Francesco Mercati
Prof. Francesco Sunseri
Guest Editors

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Keywords

Resilience
Next-generation sequencing
Omics
Biodiversity
Breeding
Phenotyping
Molecular markers

Published Papers (11 papers)

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Editorial

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4 pages, 193 KiB

Open AccessEditorial

Genetic Diversity Assessment and Marker-Assisted Selection in Crops

by Francesco Mercati and Francesco Sunseri

Genes 2020, 11(12), 1481; https://0-doi-org.brum.beds.ac.uk/10.3390/genes11121481 - 09 Dec 2020

Cited by 5 | Viewed by 1612

Abstract

Global warming is negatively impacting on crop yield and Earth’s climate changes can bring possible negative effects on the growth and reproductive success of crops [...] Full article

(This article belongs to the Special Issue Genetic Diversity Assessment and Marker-Assisted Selection in Crops)

Research

Jump to: Editorial

29 pages, 1626 KiB

Open AccessArticle

A New Intra-Specific and High-Resolution Genetic Map of Eggplant Based on a RIL Population, and Location of QTLs Related to Plant Anthocyanin Pigmentation and Seed Vigour

by Laura Toppino, Lorenzo Barchi, Francesco Mercati, Nazzareno Acciarri, Domenico Perrone, Matteo Martina, Stefano Gattolin, Tea Sala, Stefano Fadda, Antonio Mauceri, Tommaso Ciriaci, Francesco Carimi, Ezio Portis, Francesco Sunseri, Sergio Lanteri and Giuseppe Leonardo Rotino

Genes 2020, 11(7), 745; https://0-doi-org.brum.beds.ac.uk/10.3390/genes11070745 - 04 Jul 2020

Cited by 23 | Viewed by 4523

Abstract

Eggplant is the second most important solanaceous berry-producing crop after tomato. Despite mapping studies based on bi-parental progenies and GWAS approaches having been performed, an eggplant intraspecific high-resolution map is still lacking. We developed a RIL population from the intraspecific cross ‘305E40’, (androgenetic introgressed line carrying the locus Rfo-Sa1 conferring Fusarium resistance) x ‘67/3’ (breeding line whose genome sequence was recently released). One hundred and sixty-three RILs were genotyped by a genotype-by-sequencing (GBS) approach, which allowed us to identify 10,361 polymorphic sites. Overall, 267 Gb of sequencing data were generated and ~773 M Illumina paired end (PE) reads were mapped against the reference sequence. A new linkage map was developed, including 7249 SNPs assigned to the 12 chromosomes and spanning 2169.23 cM, with iaci@liberoan average distance of 0.4 cM between adjacent markers. This was used to elucidate the genetic bases of seven traits related to anthocyanin content in different organs recorded in three locations as well as seed vigor. Overall, from 7 to 17 QTLs (at least one major QTL) were identified for each trait. These results demonstrate that our newly developed map supplies valuable information for QTL fine mapping, candidate gene identification, and the development of molecular markers for marker assisted selection (MAS) of favorable alleles. Full article

(This article belongs to the Special Issue Genetic Diversity Assessment and Marker-Assisted Selection in Crops)

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23 pages, 6165 KiB

Open AccessArticle

Natural Variation Uncovers Candidate Genes for Barley Spikelet Number and Grain Yield under Drought Stress

by Samar G. Thabet, Yasser S. Moursi, Mohamed A. Karam, Andreas Börner and Ahmad M. Alqudah

Genes 2020, 11(5), 533; https://0-doi-org.brum.beds.ac.uk/10.3390/genes11050533 - 11 May 2020

Cited by 32 | Viewed by 3559

Abstract

Drought stress can occur at any growth stage and can affect crop productivity, which can result in large yield losses all over the world. In this respect, understanding the genetic architecture of agronomic traits under drought stress is essential for increasing crop yield potential and harvest. Barley is considered the most abiotic stress-tolerant cereal, particularly with respect to drought. In the present study, worldwide spring barley accessions were exposed to drought stress beginning from the early reproductive stage with 35% field capacity under field conditions. Drought stress had significantly reduced the agronomic and yield-related traits such as spike length, awn length, spikelet per spike, grains per spike and thousand kernel weight. To unravel the genetic factors underlying drought tolerance at the early reproductive stage, genome-wide association scan (GWAS) was performed using 121 spring barley accessions and a 9K single nucleotide polymorphisms (SNPs) chip. A total number of 101 significant SNPs, distributed over all seven barley chromosomes, were found to be highly associated with the studied traits, of which five genomic regions were associated with candidate genes at chromosomes 2 and 3. On chromosome 2H, the region between 6469300693-647258342 bp includes two candidate drought-specific genes (HORVU2Hr1G091030 and HORVU2Hr1G091170), which are highly associated with spikelet and final grain number per spike under drought stress conditions. Interestingly, the gene expression profile shows that the candidate genes were highly expressed in spikelet, grain, spike and leaf organs, demonstrating their pivotal role in drought tolerance. To the best of our knowledge, we reported the first detailed study that used GWAS with bioinformatic analyses to define the causative alleles and putative candidate genes underlying grain yield-related traits under field drought conditions in diverse barley germplasm. The identified alleles and candidate genes represent valuable resources for future functional characterization towards the enhancement of barley cultivars for drought tolerance. Full article

(This article belongs to the Special Issue Genetic Diversity Assessment and Marker-Assisted Selection in Crops)

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17 pages, 3243 KiB

Open AccessArticle

Molecular Analysis of the Official Algerian Olive Collection Highlighted a Hotspot of Biodiversity in the Central Mediterranean Basin

by Benalia Haddad, Alessandro Silvestre Gristina, Francesco Mercati, Abd Elkader Saadi, Nassima Aiter, Adriana Martorana, Abdoallah Sharaf and Francesco Carimi

Genes 2020, 11(3), 303; https://0-doi-org.brum.beds.ac.uk/10.3390/genes11030303 - 13 Mar 2020

Cited by 13 | Viewed by 3153

Abstract

Genetic diversity and population structure studies of local olive germplasm are important to safeguard biodiversity, for genetic resources management and to improve the knowledge on the distribution and evolution patterns of this species. In the present study Algerian olive germplasm was characterized using 16 nuclear (nuSSR) and six chloroplast (cpSSR) microsatellites. Algerian varieties, collected from the National Olive Germplasm Repository (ITAFV), 10 of which had never been genotyped before, were analyzed. Our results highlighted the presence of an exclusive genetic core represented by 13 cultivars located in a mountainous area in the North-East of Algeria, named Little Kabylie. Comparison with published datasets, representative of the Mediterranean genetic background, revealed that the most Algerian varieties showed affinity with Central and Eastern Mediterranean cultivars. Interestingly, cpSSR phylogenetic analysis supported results from nuSSRs, highlighting similarities between Algerian germplasm and wild olives from Greece, Italy, Spain and Morocco. This study sheds light on the genetic relationship of Algerian and Mediterranean olive germplasm suggesting possible events of secondary domestication and/or crossing and hybridization across the Mediterranean area. Our findings revealed a distinctive genetic background for cultivars from Little Kabylie and support the increasing awareness that North Africa represents a hotspot of diversity for crop varieties and crop wild relative species. Full article

(This article belongs to the Special Issue Genetic Diversity Assessment and Marker-Assisted Selection in Crops)

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12 pages, 1407 KiB

Open AccessArticle

Serendipitous In Situ Conservation of Faba Bean Landraces in Tunisia: A Case Study

by Elyes Babay, Khalil Khamassi, Wilma Sabetta, Monica Marilena Miazzi, Cinzia Montemurro, Domenico Pignone, Donatella Danzi, Mariella Matilde Finetti-Sialer and Giacomo Mangini

Genes 2020, 11(2), 236; https://0-doi-org.brum.beds.ac.uk/10.3390/genes11020236 - 24 Feb 2020

Cited by 8 | Viewed by 3558

Abstract

Cultivation of faba bean (Vicia faba L.) in Tunisia is largely based on improved varieties of the crop. However, a few farmers continue to produce local cultivars or landraces. The National Gene Bank of Tunisia (NGBT) recently launched a collection project for faba bean landraces, with special focus on the regions of the North West, traditionally devoted to cultivating grain legumes, and where around 80% of the total national faba bean cultivation area is located. The seed phenotypic features of the collected samples were studied, and the genetic diversity and population structure analyzed using simple sequence repeat markers. The genetic constitution of the present samples was compared to that of faba bean samples collected by teams of the International Center for Agricultural Research in the Dry Areas (ICARDA) in the 1970s in the same region, and stored at the ICARDA gene bank. The results of the diversity analysis demonstrate that the recently collected samples and those stored at ICARDA largely overlap, thus demonstrating that over the past 50 years, little genetic change has occurred to the local faba bean populations examined. These findings suggest that farmers serendipitously applied international best practices for in situ conservation of agricultural crops. Full article

(This article belongs to the Special Issue Genetic Diversity Assessment and Marker-Assisted Selection in Crops)

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13 pages, 2201 KiB

Open AccessArticle

Characteristics of Microsatellites Mined from Transcriptome Data and the Development of Novel Markers in Paeonia lactiflora

by Yingling Wan, Min Zhang, Aiying Hong, Yixuan Zhang and Yan Liu

Genes 2020, 11(2), 214; https://0-doi-org.brum.beds.ac.uk/10.3390/genes11020214 - 19 Feb 2020

Cited by 7 | Viewed by 2457

Abstract

The insufficient number of available simple sequence repeats (SSRs) inhibits genetic research on and molecular breeding of Paeonia lactiflora, a flowering crop with great economic value. The objective of this study was to develop SSRs for P. lactiflora with Illumina RNA sequencing and assess the role of SSRs in gene regulation. The results showed that dinucleotides with AG/CT repeats were the most abundant type of repeat motif in P. lactiflora and were preferentially distributed in untranslated regions. Significant differences in SSR size were observed among motif types and locations. A large number of unigenes containing SSRs participated in catalytic activity, metabolic processes and cellular processes, and 28.16% of all transcription factors and 21.74% of hub genes for inflorescence stem straightness were found to contain SSRs. Successful amplification was achieved with 89.05% of 960 pairs of SSR primers, 55.83% of which were polymorphic, and most of the 46 tested primers had a high level of transferability to the genus Paeonia. Principal component and cluster dendrogram analyses produced results consistent with known genealogical relationships. This study provides a set of SSRs with abundant information for future accession identification, marker-trait association and molecular assisted breeding in P. lactiflora. Full article

(This article belongs to the Special Issue Genetic Diversity Assessment and Marker-Assisted Selection in Crops)

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22 pages, 2673 KiB

Open AccessArticle

Genetic Analysis of QTL for Resistance to Maize Lethal Necrosis in Multiple Mapping Populations

by Luka A. O. Awata, Yoseph Beyene, Manje Gowda, Suresh L. M., McDonald B. Jumbo, Pangirayi Tongoona, Eric Danquah, Beatrice E. Ifie, Philip W. Marchelo-Dragga, Michael Olsen, Veronica Ogugo, Stephen Mugo and Boddupalli M. Prasanna

Genes 2020, 11(1), 32; https://0-doi-org.brum.beds.ac.uk/10.3390/genes11010032 - 26 Dec 2019

Cited by 18 | Viewed by 5029

Abstract

Maize lethal necrosis (MLN) occurs when maize chlorotic mottle virus (MCMV) and sugarcane mosaic virus (SCMV) co-infect maize plant. Yield loss of up to 100% can be experienced under severe infections. Identification and validation of genomic regions and their flanking markers can facilitate marker assisted breeding for resistance to MLN. To understand the status of previously identified quantitative trait loci (QTL)in diverse genetic background, F₃ progenies derived from seven bi-parental populations were genotyped using 500 selected kompetitive allele specific PCR (KASP) SNPs. The F₃ progenies were evaluated under artificial MLN inoculation for three seasons. Phenotypic analyses revealed significant variability (P ≤ 0.01) among genotypes for responses to MLN infections, with high heritability estimates (0.62 to 0.82) for MLN disease severity and AUDPC values. Linkage mapping and joint linkage association mapping revealed at least seven major QTL (qMLN3_130 and qMLN3_142, qMLN5_190 and qMLN5_202, qMLN6_85 and qMLN6_157 qMLN8_10 and qMLN9_142) spread across the 7-biparetal populations, for resistance to MLN infections and were consistent with those reported previously. The seven QTL appeared to be stable across genetic backgrounds and across environments. Therefore, these QTL could be useful for marker assisted breeding for resistance to MLN. Full article

(This article belongs to the Special Issue Genetic Diversity Assessment and Marker-Assisted Selection in Crops)

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24 pages, 781 KiB

Open AccessArticle

Transferability and Polymorphism of SSR Markers Located in Flavonoid Pathway Genes in Fragaria and Rubus Species

by Vadim G. Lebedev, Natalya M. Subbotina, Oleg P. Maluchenko, Tatyana N. Lebedeva, Konstantin V. Krutovsky and Konstantin A. Shestibratov

Genes 2020, 11(1), 11; https://0-doi-org.brum.beds.ac.uk/10.3390/genes11010011 - 21 Dec 2019

Cited by 23 | Viewed by 3898

Abstract

Strawberry (Fragaria) and raspberry (Rubus) are very popular crops, and improving their nutritional quality and disease resistance are important tasks in their breeding programs that are becoming increasingly based on use of functional DNA markers. We identified 118 microsatellite (simple sequence repeat—SSR) loci in the nucleotide sequences of flavonoid biosynthesis and pathogenesis-related genes and developed 24 SSR markers representing some of these structural and regulatory genes. These markers were used to assess the genetic diversity of 48 Fragaria and Rubus specimens, including wild species and rare cultivars, which differ in berry color, ploidy, and origin. We have demonstrated that a high proportion of the developed markers are transferable within and between Fragaria and Rubus genera and are polymorphic. Transferability and polymorphism of the SSR markers depended on location of their polymerase chain reaction (PCR) primer annealing sites and microsatellite loci in genes, respectively. High polymorphism of the SSR markers in regulatory flavonoid biosynthesis genes suggests their allelic variability that can be potentially associated with differences in flavonoid accumulation and composition. This set of SSR markers may be a useful molecular tool in strawberry and raspberry breeding programs for improvement anthocyanin related traits. Full article

(This article belongs to the Special Issue Genetic Diversity Assessment and Marker-Assisted Selection in Crops)

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12 pages, 3448 KiB

Open AccessArticle

The Molecular Determination of Hybridity and Homozygosity Estimates in Breeding Populations of Lettuce (Lactuca sativa L.)

by Alice Patella, Fabio Palumbo, Giulio Galla and Gianni Barcaccia

Genes 2019, 10(11), 916; https://0-doi-org.brum.beds.ac.uk/10.3390/genes10110916 - 09 Nov 2019

Cited by 14 | Viewed by 3336

Abstract

The development of new varieties of horticultural crops benefits from the integration of conventional and molecular marker-assisted breeding schemes in order to combine phenotyping and genotyping information. In this study, a selected panel of 16 microsatellite markers were used in different steps of a breeding programme of lettuce (Lactuca sativa L., 2 n = 18). Molecular markers were first used to genotype 71 putative parental lines and to plan 89 controlled crosses designed to maximise recombination potentials. The resulting 871 progeny plants were then molecularly screened, and their marker allele profiles were compared with the profiles expected based on the parental lines. The average cross-pollination success rate was 68 ± 33%, so 602 F1 hybrids were completely identified. Unexpected genotypes were detected in 5% of cases, consistent with this species’ spontaneous out-pollination rate. Finally, in a later step of the breeding programme, 47 different F3 progenies, selected by phenotyping for a number of morphological descriptors, were characterised in terms of their observed homozygosity and within-population genetic uniformity and stability. Ten of these populations had a median homozygosity above 90% and a median genetic similarity above 95% and are, therefore, particularly suitable for pre-commercial trials. In conclusion, this study shows the synergistic effects and advantages of conventional and molecular methods of selection applied in different steps of a breeding programme aimed at developing new varieties of lettuce. Full article

(This article belongs to the Special Issue Genetic Diversity Assessment and Marker-Assisted Selection in Crops)

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19 pages, 1542 KiB

Open AccessArticle

Diversity Analysis of Sweet Potato Genetic Resources Using Morphological and Qualitative Traits and Molecular Markers

by Fabio Palumbo, Aline Carolina Galvao, Carlo Nicoletto, Paolo Sambo and Gianni Barcaccia

Genes 2019, 10(11), 840; https://0-doi-org.brum.beds.ac.uk/10.3390/genes10110840 - 24 Oct 2019

Cited by 17 | Viewed by 4243

Abstract

The European Union (EU) market for sweet potatoes has increased by 100% over the last five years, and sweet potato cultivation in southern European countries is a new opportunity for the EU to exploit and introduce new genotypes. In view of this demand, the origins of the principal Italian sweet potato clones, compared with a core collection of genotypes from Central and Southern America, were investigated for the first time. This was accomplished by combining a genetic analysis, exploiting 14 hypervariable microsatellite markers, with morphological and chemical measurements based on 16 parameters. From the molecular analyses, Italian accessions were determined to be genetically very similar to the South American germplasm, but they were sub-clustered into two groups. This finding was subsequently confirmed by the morphological and chemical measurements. Moreover, the analysis of the genetic structure of the population suggested that one of the two groups of Italian genotypes may have descended from one of the South American accessions, as predicted on the basis of the shared morphological characteristics and molecular fingerprints. Overall, the combination of two different characterization methods, genetic markers and agronomic traits, was effective in differentiating or clustering the sweet potato genotypes, in agreement with their geographical origin or phenotypic descriptors. This information could be exploited by both breeders and farmers to detect and protect commercial varieties, and hence for traceability purposes. Full article

(This article belongs to the Special Issue Genetic Diversity Assessment and Marker-Assisted Selection in Crops)

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12 pages, 1511 KiB

Open AccessArticle

Natural Variation and Domestication Selection of ZmPGP1 Affects Plant Architecture and Yield-Related Traits in Maize

by Pengcheng Li, Jie Wei, Houmiao Wang, Yuan Fang, Shuangyi Yin, Yang Xu, Jun Liu, Zefeng Yang and Chenwu Xu

Genes 2019, 10(9), 664; https://0-doi-org.brum.beds.ac.uk/10.3390/genes10090664 - 30 Aug 2019

Cited by 22 | Viewed by 3115

Abstract

ZmPGP1, involved in the polar auxin transport, has been shown to be associated with plant height, leaf angle, yield traits, and root development in maize. To explore natural variation and domestication selection of ZmPGP1, we re-sequenced the ZmPGP1 gene in 349 inbred lines, 68 landraces, and 32 teosintes. Sequence polymorphisms, nucleotide diversity, and neutral tests revealed that ZmPGP1 might be selected during domestication and improvement processes. Marker–trait association analysis in inbred lines identified 11 variants significantly associated with 4 plant architecture and 5 ear traits. SNP1473 was the most significant variant for kernel length and ear grain weight. The frequency of an increased allele T was 40.6% in teosintes, and it was enriched to 60.3% and 89.1% during maize domestication and improvement. This result revealed that ZmPGP1 may be selected in the domestication and improvement process, and significant variants could be used to develop functional markers to improve plant architecture and ear traits in maize. Full article

(This article belongs to the Special Issue Genetic Diversity Assessment and Marker-Assisted Selection in Crops)

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