International Journal of Molecular Sciences

Editorial

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5 pages, 226 KiB

Open AccessEditorial

Legume Genetics and Biology: From Mendel’s Pea to Legume Genomics

by Petr Smýkal, Eric J.B. von Wettberg and Kevin McPhee

Int. J. Mol. Sci. 2020, 21(9), 3336; https://doi.org/10.3390/ijms21093336 - 8 May 2020

Cited by 8 | Viewed by 5566

Abstract

Legumes have played an important part in cropping systems since the dawn of agriculture, both as human food and as animal feed. The legume family is arguably one of the most abundantly domesticated crop plant families. Their ability to symbiotically fix nitrogen and [...] Read more.

Legumes have played an important part in cropping systems since the dawn of agriculture, both as human food and as animal feed. The legume family is arguably one of the most abundantly domesticated crop plant families. Their ability to symbiotically fix nitrogen and improve soil fertility has been rewarded since antiquity and makes them a key protein source. The pea was the original model organism used in Mendel’s discovery of the laws of inheritance, making it the foundation of modern plant genetics. This Special Issue provides up-to-date information on legume biology, genetic advances, and the legacy of Mendel. Full article

(This article belongs to the Special Issue Legume Genetics and Biology: From Mendel's Pea to Legume Genomics)

Research

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17 pages, 4586 KiB

Open AccessArticle

Genomic Analysis of Vavilov’s Historic Chickpea Landraces Reveals Footprints of Environmental and Human Selection

by Alena Sokolkova, Sergey V. Bulyntsev, Peter L. Chang, Noelia Carrasquilla-Garcia, Anna A. Igolkina, Nina V. Noujdina, Eric von Wettberg, Margarita A. Vishnyakova, Douglas R. Cook, Sergey V. Nuzhdin and Maria G. Samsonova

Int. J. Mol. Sci. 2020, 21(11), 3952; https://doi.org/10.3390/ijms21113952 - 31 May 2020

Cited by 14 | Viewed by 3502

Abstract

A defining challenge of the 21st century is meeting the nutritional demands of the growing human population, under a scenario of limited land and water resources and under the specter of climate change. The Vavilov seed bank contains numerous landraces collected nearly a [...] Read more.

A defining challenge of the 21st century is meeting the nutritional demands of the growing human population, under a scenario of limited land and water resources and under the specter of climate change. The Vavilov seed bank contains numerous landraces collected nearly a hundred years ago, and thus may contain ‘genetic gems’ with the potential to enhance modern breeding efforts. Here, we analyze 407 landraces, sampled from major historic centers of chickpea cultivation and secondary diversification. Genome-Wide Association Studies (GWAS) conducted on both phenotypic traits and bioclimatic variables at landraces sampling sites as extended phenotypes resulted in 84 GWAS hits associated to various regions. The novel haploblock-based test identified haploblocks enriched for single nucleotide polymorphisms (SNPs) associated with phenotypes and bioclimatic variables. Subsequent bi-clustering of traits sharing enriched haploblocks underscored both non-random distribution of SNPs among several haploblocks and their association with multiple traits. We hypothesize that these clusters of pleiotropic SNPs represent co-adapted genetic complexes to a range of environmental conditions that chickpea experienced during domestication and subsequent geographic radiation. Linking genetic variation to phenotypic data and a wealth of historic information preserved in historic seed banks are the keys for genome-based and environment-informed breeding intensification. Full article

(This article belongs to the Special Issue Legume Genetics and Biology: From Mendel's Pea to Legume Genomics)

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20 pages, 605 KiB

Open AccessArticle

Development and Proof-of-Concept Application of Genome-Enabled Selection for Pea Grain Yield under Severe Terminal Drought

by Paolo Annicchiarico, Nelson Nazzicari, Meriem Laouar, Imane Thami-Alami, Massimo Romani and Luciano Pecetti

Int. J. Mol. Sci. 2020, 21(7), 2414; https://doi.org/10.3390/ijms21072414 - 31 Mar 2020

Cited by 19 | Viewed by 2920

Abstract

Terminal drought is the main stress limiting pea (Pisum sativum L.) grain yield in Mediterranean environments. This study aimed to investigate genotype × environment (GE) interaction patterns, define a genomic selection (GS) model for yield under severe drought based on single nucleotide [...] Read more.

Terminal drought is the main stress limiting pea (Pisum sativum L.) grain yield in Mediterranean environments. This study aimed to investigate genotype × environment (GE) interaction patterns, define a genomic selection (GS) model for yield under severe drought based on single nucleotide polymorphism (SNP) markers from genotyping-by-sequencing, and compare GS with phenotypic selection (PS) and marker-assisted selection (MAS). Some 288 lines belonging to three connected RIL populations were evaluated in a managed-stress (MS) environment of Northern Italy, Marchouch (Morocco), and Alger (Algeria). Intra-environment, cross-environment, and cross-population predictive ability were assessed by Ridge Regression best linear unbiased prediction (rrBLUP) and Bayesian Lasso models. GE interaction was particularly large across moderate-stress and severe-stress environments. In proof-of-concept experiments performed in a MS environment, GS models constructed from MS environment and Marchouch data applied to independent material separated top-performing lines from mid- and bottom-performing ones, and produced actual yield gains similar to PS. The latter result would imply somewhat greater GS efficiency when considering same selection costs, in partial agreement with predicted efficiency results. GS, which exploited drought escape and intrinsic drought tolerance, exhibited 18% greater selection efficiency than MAS (albeit with non-significant difference between selections) and moderate to high cross-population predictive ability. GS can be cost-efficient to raise yields under severe drought. Full article

(This article belongs to the Special Issue Legume Genetics and Biology: From Mendel's Pea to Legume Genomics)

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26 pages, 2526 KiB

Open AccessArticle

Genome-Wide Association Mapping for Heat Stress Responsive Traits in Field Pea

by Endale G. Tafesse, Krishna K. Gali, V.B. Reddy Lachagari, Rosalind Bueckert and Thomas D. Warkentin

Int. J. Mol. Sci. 2020, 21(6), 2043; https://doi.org/10.3390/ijms21062043 - 17 Mar 2020

Cited by 36 | Viewed by 4816

Abstract

Environmental stress hampers pea productivity. To understand the genetic basis of heat resistance, a genome-wide association study (GWAS) was conducted on six stress responsive traits of physiological and agronomic importance in pea, with an objective to identify the genetic loci associated with these [...] Read more.

Environmental stress hampers pea productivity. To understand the genetic basis of heat resistance, a genome-wide association study (GWAS) was conducted on six stress responsive traits of physiological and agronomic importance in pea, with an objective to identify the genetic loci associated with these traits. One hundred and thirty-five genetically diverse pea accessions from major pea growing areas of the world were phenotyped in field trials across five environments, under generally ambient (control) and heat stress conditions. Statistical analysis of phenotype indicated significant effects of genotype (G), environment (E), and G × E interaction for all traits. A total of 16,877 known high-quality SNPs were used for association analysis to determine marker-trait associations (MTA). We identified 32 MTAs that were consistent in at least three environments for association with the traits of stress resistance: six for chlorophyll concentration measured by a soil plant analysis development meter; two each for photochemical reflectance index and canopy temperature; seven for reproductive stem length; six for internode length; and nine for pod number. Forty-eight candidate genes were identified within 15 kb distance of these markers. The identified markers and candidate genes have potential for marker-assisted selection towards the development of heat resistant pea cultivars. Full article

(This article belongs to the Special Issue Legume Genetics and Biology: From Mendel's Pea to Legume Genomics)

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27 pages, 4139 KiB

Open AccessArticle

Reconstruction of the Evolutionary Histories of UGT Gene Superfamily in Legumes Clarifies the Functional Divergence of Duplicates in Specialized Metabolism

by Panneerselvam Krishnamurthy, Chigen Tsukamoto and Masao Ishimoto

Int. J. Mol. Sci. 2020, 21(5), 1855; https://doi.org/10.3390/ijms21051855 - 8 Mar 2020

Cited by 14 | Viewed by 4521

Abstract

Plant uridine 5′-diphosphate glycosyltransferases (UGTs) influence the physiochemical properties of several classes of specialized metabolites including triterpenoids via glycosylation. To uncover the evolutionary past of UGTs of soyasaponins (a group of beneficial triterpene glycosides widespread among Leguminosae), the UGT gene superfamily in Medicago [...] Read more.

Plant uridine 5′-diphosphate glycosyltransferases (UGTs) influence the physiochemical properties of several classes of specialized metabolites including triterpenoids via glycosylation. To uncover the evolutionary past of UGTs of soyasaponins (a group of beneficial triterpene glycosides widespread among Leguminosae), the UGT gene superfamily in Medicago truncatula, Glycine max, Phaseolus vulgaris, Lotus japonicus, and Trifolium pratense genomes were systematically mined. A total of 834 nonredundant UGTs were identified and categorized into 98 putative orthologous loci (POLs) using tree-based and graph-based methods. Major key findings in this study were of, (i) 17 POLs represent potential catalysts for triterpene glycosylation in legumes, (ii) UGTs responsible for the addition of second (UGT73P2: galactosyltransferase and UGT73P10: arabinosyltransferase) and third (UGT91H4: rhamnosyltransferase and UGT91H9: glucosyltransferase) sugars of the C-3 sugar chain of soyasaponins were resulted from duplication events occurred before and after the hologalegina–millettoid split, respectively, and followed neofunctionalization in species-/ lineage-specific manner, and (iii) UGTs responsible for the C-22-O glycosylation of group A (arabinosyltransferase) and DDMP saponins (DDMPtransferase) and the second sugar of C-22 sugar chain of group A saponins (UGT73F2: glucosyltransferase) may all share a common ancestor. Our findings showed a way to trace the evolutionary history of UGTs involved in specialized metabolism. Full article

(This article belongs to the Special Issue Legume Genetics and Biology: From Mendel's Pea to Legume Genomics)

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36 pages, 3754 KiB

Open AccessArticle

High-Resolution Mapping in Two RIL Populations Refines Major “QTL Hotspot” Regions for Seed Size and Shape in Soybean (Glycine max L.)

by Aiman Hina, Yongce Cao, Shiyu Song, Shuguang Li, Ripa Akter Sharmin, Mahmoud A. Elattar, Javaid Akhter Bhat and Tuanjie Zhao

Int. J. Mol. Sci. 2020, 21(3), 1040; https://doi.org/10.3390/ijms21031040 - 4 Feb 2020

Cited by 52 | Viewed by 4642

Abstract

Seed size and shape are important traits determining yield and quality in soybean. However, the genetic mechanism and genes underlying these traits remain largely unexplored. In this regard, this study used two related recombinant inbred line (RIL) populations (ZY and K3N) evaluated in [...] Read more.

Seed size and shape are important traits determining yield and quality in soybean. However, the genetic mechanism and genes underlying these traits remain largely unexplored. In this regard, this study used two related recombinant inbred line (RIL) populations (ZY and K3N) evaluated in multiple environments to identify main and epistatic-effect quantitative trait loci (QTLs) for six seed size and shape traits in soybean. A total of 88 and 48 QTLs were detected through composite interval mapping (CIM) and mixed-model-based composite interval mapping (MCIM), respectively, and 15 QTLs were common among both methods; two of them were major (R² > 10%) and novel QTLs (viz., qSW-1-1_ZN and qSLT-20-1_K3N). Additionally, 51 and 27 QTLs were identified for the first time through CIM and MCIM methods, respectively. Colocalization of QTLs occurred in four major QTL hotspots/clusters, viz., “QTL Hotspot A”, “QTL Hotspot B”, “QTL Hotspot C”, and “QTL Hotspot D” located on Chr06, Chr10, Chr13, and Chr20, respectively. Based on gene annotation, gene ontology (GO) enrichment, and RNA-Seq analysis, 23 genes within four “QTL Hotspots” were predicted as possible candidates, regulating soybean seed size and shape. Network analyses demonstrated that 15 QTLs showed significant additive x environment (AE) effects, and 16 pairs of QTLs showing epistatic effects were also detected. However, except three epistatic QTLs, viz., qSL-13-3_ZY, qSL-13-4_ZY_, and qSW-13-4_ZY, all the remaining QTLs depicted no main effects. Hence, the present study is a detailed and comprehensive investigation uncovering the genetic basis of seed size and shape in soybeans. The use of a high-density map identified new genomic regions providing valuable information and could be the primary target for further fine mapping, candidate gene identification, and marker-assisted breeding (MAB). Full article

(This article belongs to the Special Issue Legume Genetics and Biology: From Mendel's Pea to Legume Genomics)

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19 pages, 1722 KiB

Open AccessArticle

A Combined Linkage and GWAS Analysis Identifies QTLs Linked to Soybean Seed Protein and Oil Content

by Tengfei Zhang, Tingting Wu, Liwei Wang, Bingjun Jiang, Caixin Zhen, Shan Yuan, Wensheng Hou, Cunxiang Wu, Tianfu Han and Shi Sun

Int. J. Mol. Sci. 2019, 20(23), 5915; https://doi.org/10.3390/ijms20235915 - 25 Nov 2019

Cited by 45 | Viewed by 5912

Abstract

Soybean is an excellent source of vegetable protein and edible oil. Understanding the genetic basis of protein and oil content will improve the breeding programs for soybean. Linkage analysis and genome-wide association study (GWAS) tools were combined to detect quantitative trait loci (QTL) [...] Read more.

Soybean is an excellent source of vegetable protein and edible oil. Understanding the genetic basis of protein and oil content will improve the breeding programs for soybean. Linkage analysis and genome-wide association study (GWAS) tools were combined to detect quantitative trait loci (QTL) that are associated with protein and oil content in soybean. Three hundred and eight recombinant inbred lines (RILs) containing 3454 single nucleotide polymorphism (SNP) markers and 200 soybean accessions, including 94,462 SNPs and indels, were applied to identify QTL intervals and significant SNP loci. Intervals on chromosomes 1, 15, and 20 were correlated with both traits, and QTL qPro15-1, qPro20-1, and qOil5-1 reproducibly correlated with large phenotypic variations. SNP loci on chromosome 20 that overlapped with qPro20-1 were reproducibly connected to both traits by GWAS (p < 10⁻⁴). Twenty-five candidate genes with putative roles in protein and/or oil metabolisms within two regions (qPro15-1, qPro20-1) were identified, and eight of these genes showed differential expressions in parent lines during late reproductive growth stages, consistent with a role in controlling protein and oil content. The new well-defined QTL should significantly improve molecular breeding programs, and the identified candidate genes may help elucidate the mechanisms of protein and oil biosynthesis. Full article

(This article belongs to the Special Issue Legume Genetics and Biology: From Mendel's Pea to Legume Genomics)

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23 pages, 1858 KiB

Open AccessArticle

Candidate Domestication-Related Genes Revealed by Expression Quantitative Trait Loci Mapping of Narrow-Leafed Lupin (Lupinus angustifolius L.)

by Piotr Plewiński, Michał Książkiewicz, Sandra Rychel-Bielska, Elżbieta Rudy and Bogdan Wolko

Int. J. Mol. Sci. 2019, 20(22), 5670; https://doi.org/10.3390/ijms20225670 - 12 Nov 2019

Cited by 22 | Viewed by 3992

Abstract

The last century has witnessed rapid domestication of the narrow-leafed lupin (Lupinus angustifolius L.) as a grain legume crop, exploiting discovered alleles conferring low-alkaloid content (iucundus), vernalization independence (Ku and Julius), and reduced pod shattering (lentus and [...] Read more.

The last century has witnessed rapid domestication of the narrow-leafed lupin (Lupinus angustifolius L.) as a grain legume crop, exploiting discovered alleles conferring low-alkaloid content (iucundus), vernalization independence (Ku and Julius), and reduced pod shattering (lentus and tardus). In this study, a L. angustifolius mapping population was subjected to massive analysis of cDNA ends (MACE). The MACE yielded 4185 single nucleotide polymorphism (SNP) markers for linkage map improvement and 30,595 transcriptomic profiles for expression quantitative trait loci (eQTL) mapping. The eQTL highlighted a high number of cis- and trans-regulated alkaloid biosynthesis genes with gene expression orchestrated by a regulatory agent localized at iucundus locus, supporting the concept that ETHYLENE RESPONSIVE TRANSCRIPTION FACTOR RAP2-7 may control low-alkaloid phenotype. The analysis of Ku shed light on the vernalization response via FLOWERING LOCUS T and FD regulon in L. angustifolius, providing transcriptomic evidence for the contribution of several genes acting in C-repeat binding factor (CBF) cold responsiveness and in UDP-glycosyltransferases pathways. Research on lentus selected a DUF1218 domain protein as a candidate gene controlling the orientation of the sclerified endocarp and a homolog of DETOXIFICATION14 for purplish hue of young pods. An ABCG transporter was identified as a hypothetical contributor to sclerenchyma fortification underlying tardus phenotype. Full article

(This article belongs to the Special Issue Legume Genetics and Biology: From Mendel's Pea to Legume Genomics)

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33 pages, 2223 KiB

Open AccessArticle

Functional Dissection of the Chickpea (Cicer arietinum L.) Stay-Green Phenotype Associated with Molecular Variation at an Ortholog of Mendel’s I Gene for Cotyledon Color: Implications for Crop Production and Carotenoid Biofortification

by Kaliamoorthy Sivasakthi, Edward Marques, Ng’andwe Kalungwana, Noelia Carrasquilla-Garcia, Peter L. Chang, Emily M. Bergmann, Erika Bueno, Matilde Cordeiro, Syed Gul A.S. Sani, Sripada M. Udupa, Irshad A. Rather, Reyazul Rouf Mir, Vincent Vadez, George J. Vandemark, Pooran M. Gaur, Douglas R. Cook, Christine Boesch, Eric J.B. von Wettberg, Jana Kholova and R. Varma Penmetsa

Int. J. Mol. Sci. 2019, 20(22), 5562; https://doi.org/10.3390/ijms20225562 - 7 Nov 2019

Cited by 15 | Viewed by 5999

Abstract

“Stay-green” crop phenotypes have been shown to impact drought tolerance and nutritional content of several crops. We aimed to genetically describe and functionally dissect the particular stay-green phenomenon found in chickpeas with a green cotyledon color of mature dry seed and investigate its [...] Read more.

“Stay-green” crop phenotypes have been shown to impact drought tolerance and nutritional content of several crops. We aimed to genetically describe and functionally dissect the particular stay-green phenomenon found in chickpeas with a green cotyledon color of mature dry seed and investigate its potential use for improvement of chickpea environmental adaptations and nutritional value. We examined 40 stay-green accessions and a set of 29 BC2F4-5 stay-green introgression lines using a stay-green donor parent ICC 16340 and two Indian elite cultivars (KAK2, JGK1) as recurrent parents. Genetic studies of segregating populations indicated that the green cotyledon trait is controlled by a single recessive gene that is invariantly associated with the delayed degreening (extended chlorophyll retention). We found that the chickpea ortholog of Mendel’s I locus of garden pea, encoding a SGR protein as very likely to underlie the persistently green cotyledon color phenotype of chickpea. Further sequence characterization of this chickpea ortholog CaStGR1 (CaStGR1, for carietinum stay-green gene 1) revealed the presence of five different molecular variants (alleles), each of which is likely a loss-of-function of the chickpea protein (CaStGR1) involved in chlorophyll catabolism. We tested the wild type and green cotyledon lines for components of adaptations to dry environments and traits linked to agronomic performance in different experimental systems and different levels of water availability. We found that the plant processes linked to disrupted CaStGR1 gene did not functionality affect transpiration efficiency or water usage. Photosynthetic pigments in grains, including provitaminogenic carotenoids important for human nutrition, were 2–3-fold higher in the stay-green type. Agronomic performance did not appear to be correlated with the presence/absence of the stay-green allele. We conclude that allelic variation in chickpea CaStGR1 does not compromise traits linked to environmental adaptation and agronomic performance, and is a promising genetic technology for biofortification of provitaminogenic carotenoids in chickpea. Full article

(This article belongs to the Special Issue Legume Genetics and Biology: From Mendel's Pea to Legume Genomics)

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21 pages, 3716 KiB

Open AccessArticle

Irrigation-Induced Changes in Chemical Composition and Quality of Seeds of Yellow Lupine (Lupinus luteus L.)

by Justyna T. Polit, Iwona Ciereszko, Alina T. Dubis, Joanna Leśniewska, Anna Basa, Konrad Winnicki, Aneta Żabka, Marharyta Audzei, Łukasz Sobiech, Agnieszka Faligowska, Grzegorz Skrzypczak and Janusz Maszewski

Int. J. Mol. Sci. 2019, 20(22), 5521; https://doi.org/10.3390/ijms20225521 - 6 Nov 2019

Cited by 4 | Viewed by 4048

Abstract

The quality and amount of yellow lupine yield depend on water availability. Water scarcity negatively affects germination, flowering, and pod formation, and thus introduction of an artificial irrigation system is needed. The aim of this study was to evaluate the influence of irrigation [...] Read more.

The quality and amount of yellow lupine yield depend on water availability. Water scarcity negatively affects germination, flowering, and pod formation, and thus introduction of an artificial irrigation system is needed. The aim of this study was to evaluate the influence of irrigation on the quality of yellow lupine seeds. Raining was applied with a semi-solid device with sprinklers during periods of greatest water demand. It was shown that watered plants produced seeds of lesser quality, having smaller size and weight. To find out why seeds of irrigated plants were of poor quality, interdisciplinary research at the cellular level was carried out. DNA cytophotometry evidenced the presence of nuclei with lower polyploidy in the apical zone of mature seeds. This may lead to formation of smaller cells and reduce depositing of storage materials. The electrophoretic and Fourier transform infrared spectroscopic analyses revealed differences in protein and cuticular wax profiles, while scanning electron microscopy and energy dispersive spectroscopy revealed, among various chemical elements, decreased calcium content in one of seed zones (near plumule). Seeds from irrigated plants showed slightly higher germination dynamics but growth rate of seedlings was slightly lower. The studies showed that irrigation of lupine affected seed features and their chemical composition, an ability to germination and seedlings growth. Full article

(This article belongs to the Special Issue Legume Genetics and Biology: From Mendel's Pea to Legume Genomics)

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26 pages, 4277 KiB

Open AccessArticle

Allelic Variants for Candidate Nitrogen Fixation Genes Revealed by Sequencing in Red Clover (Trifolium pratense L.)

by Oldřich Trněný, David Vlk, Eliška Macková, Michaela Matoušková, Jana Řepková, Jan Nedělník, Jan Hofbauer, Karel Vejražka, Hana Jakešová, Jan Jansa, Lubomír Piálek and Daniela Knotová

Int. J. Mol. Sci. 2019, 20(21), 5470; https://doi.org/10.3390/ijms20215470 - 2 Nov 2019

Cited by 8 | Viewed by 4074

Abstract

Plant–rhizobia symbiosis can activate key genes involved in regulating nodulation associated with biological nitrogen fixation (BNF). Although the general molecular basis of the BNF process is frequently studied, little is known about its intraspecific variability and the characteristics of its allelic variants. This [...] Read more.

Plant–rhizobia symbiosis can activate key genes involved in regulating nodulation associated with biological nitrogen fixation (BNF). Although the general molecular basis of the BNF process is frequently studied, little is known about its intraspecific variability and the characteristics of its allelic variants. This study’s main goals were to describe phenotypic and genotypic variation in the context of nitrogen fixation in red clover (Trifolium pretense L.) and identify variants in BNF candidate genes associated with BNF efficiency. Acetylene reduction assay validation was the criterion for selecting individual plants with particular BNF rates. Sequences in 86 key candidate genes were obtained by hybridization-based sequence capture target enrichment of plants with alternative phenotypes for nitrogen fixation. Two genes associated with BNF were identified: ethylene response factor required for nodule differentiation (EFD) and molybdate transporter 1 (MOT1). In addition, whole-genome population genotyping by double-digest restriction-site-associated sequencing (ddRADseq) was performed, and BNF was evaluated by the natural ¹⁵N abundance method. Polymorphisms associated with BNF and reflecting phenotype variability were identified. The genetic structure of plant accessions was not linked to BNF rate of measured plants. Knowledge of the genetic variation within BNF candidate genes and the characteristics of genetic variants will be beneficial in molecular diagnostics and breeding of red clover. Full article

(This article belongs to the Special Issue Legume Genetics and Biology: From Mendel's Pea to Legume Genomics)

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40 pages, 6750 KiB

Open AccessArticle

Integrated Analysis of Small RNA, Transcriptome and Degradome Sequencing Provides New Insights into Floral Development and Abscission in Yellow Lupine (Lupinus luteus L.)

by Paulina Glazińska, Milena Kulasek, Wojciech Glinkowski, Waldemar Wojciechowski and Jan Kosiński

Int. J. Mol. Sci. 2019, 20(20), 5122; https://doi.org/10.3390/ijms20205122 - 16 Oct 2019

Cited by 18 | Viewed by 4371

Abstract

The floral development in an important legume crop yellow lupine (Lupinus luteus L., Taper cv.) is often affected by the abscission of flowers leading to significant economic losses. Small non-coding RNAs (sncRNAs), which have a proven effect on almost all developmental processes [...] Read more.

The floral development in an important legume crop yellow lupine (Lupinus luteus L., Taper cv.) is often affected by the abscission of flowers leading to significant economic losses. Small non-coding RNAs (sncRNAs), which have a proven effect on almost all developmental processes in other plants, might be of key players in a complex net of molecular interactions regulating flower development and abscission. This study represents the first comprehensive sncRNA identification and analysis of small RNA, transcriptome and degradome sequencing data in lupine flowers to elucidate their role in the regulation of lupine generative development. As shedding in lupine primarily concerns flowers formed at the upper part of the inflorescence, we analyzed samples from extreme parts of raceme separately and conducted an additional analysis of pedicels from abscising and non-abscising flowers where abscission zone forms. A total of 394 known and 28 novel miRNAs and 316 phased siRNAs were identified. In flowers at different stages of development 59 miRNAs displayed differential expression (DE) and 46 DE miRNAs were found while comparing the upper and lower flowers. Identified tasiR-ARFs were DE in developing flowers and were strongly expressed in flower pedicels. The DEmiR-targeted genes were preferentially enriched in the functional categories related to carbohydrate metabolism and plant hormone transduction pathways. This study not only contributes to the current understanding of how lupine flowers develop or undergo abscission but also holds potential for research aimed at crop improvement. Full article

(This article belongs to the Special Issue Legume Genetics and Biology: From Mendel's Pea to Legume Genomics)

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16 pages, 2707 KiB

Open AccessArticle

Two Novel er1 Alleles Conferring Powdery Mildew (Erysiphe pisi) Resistance Identified in a Worldwide Collection of Pea (Pisum sativum L.) Germplasms

by Suli Sun, Dong Deng, Canxing Duan, Xuxiao Zong, Dongxu Xu, Yuhua He and Zhendong Zhu

Int. J. Mol. Sci. 2019, 20(20), 5071; https://doi.org/10.3390/ijms20205071 - 12 Oct 2019

Cited by 20 | Viewed by 3328

Abstract

Powdery mildew caused by Erysiphe pisi DC. severely affects pea crops worldwide. The use of resistant cultivars containing the er1 gene is the most effective way to control this disease. The objectives of this study were to reveal er1 alleles contained in 55 [...] Read more.

Powdery mildew caused by Erysiphe pisi DC. severely affects pea crops worldwide. The use of resistant cultivars containing the er1 gene is the most effective way to control this disease. The objectives of this study were to reveal er1 alleles contained in 55 E. pisi-resistant pea germplasms and to develop the functional markers of novel alleles. Sequences of 10 homologous PsMLO1 cDNA clones from each germplasm accession were used to determine their er1 alleles. The frame shift mutations and various alternative splicing patterns were observed during transcription of the er1 gene. Two novel er1 alleles, er1-8 and er1-9, were discovered in the germplasm accessions G0004839 and G0004400, respectively, and four known er1 alleles were identified in 53 other accessions. One mutation in G0004839 was characterized by a 3-bp (GTG) deletion of the wild-type PsMLO1 cDNA, resulting in a missing valine at position 447 of the PsMLO1 protein sequence. Another mutation in G0004400 was caused by a 1-bp (T) deletion of the wild-type PsMLO1 cDNA sequence, resulting in a serine to leucine change of the PsMLO1 protein sequence. The er1-8 and er1-9 alleles were verified using resistance inheritance analysis and genetic mapping with respectively derived F₂ and F_2:3 populations. Finally, co-dominant functional markers specific to er1-8 and er1-9 were developed and validated in populations and pea germplasms. These results improve our understanding of E. pisi resistance in pea germplasms worldwide and provide powerful tools for marker-assisted selection in pea breeding. Full article

(This article belongs to the Special Issue Legume Genetics and Biology: From Mendel's Pea to Legume Genomics)

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23 pages, 5284 KiB

Open AccessArticle

Characterization and Rapid Gene-Mapping of Leaf Lesion Mimic Phenotype of spl-1 Mutant in Soybean (Glycine max (L.) Merr.)

by G M Al Amin, Keke Kong, Ripa Akter Sharmin, Jiejie Kong, Javaid Akhter Bhat and Tuanjie Zhao

Int. J. Mol. Sci. 2019, 20(9), 2193; https://doi.org/10.3390/ijms20092193 - 3 May 2019

Cited by 27 | Viewed by 5408

Abstract

In plants, lesion mimic mutants (LMMs) reveal spontaneous disease-like lesions in the absence of pathogen that constitutes powerful genetic material to unravel genes underlying programmed cell death (PCD), particularly the hypersensitive response (HR). However, only a few LMMs are reported in soybean, and [...] Read more.

In plants, lesion mimic mutants (LMMs) reveal spontaneous disease-like lesions in the absence of pathogen that constitutes powerful genetic material to unravel genes underlying programmed cell death (PCD), particularly the hypersensitive response (HR). However, only a few LMMs are reported in soybean, and no related gene has been cloned until now. In the present study, we isolated a new LMM named spotted leaf-1 (spl-1) from NN1138-2 cultivar through ethyl methanesulfonate (EMS) treatment. The present study revealed that lesion formation might result from PCD and excessive reactive oxygen species (ROS) accumulation. The chlorophyll content was significantly reduced but antioxidant activities, viz., superoxide dismutase (SOD), peroxidase (POD) and catalase (CAT), as well as the malondialdehyde (MDA) contents, were detected higher in spl-1 than in the wild-type. According to segregation analysis of mutant phenotype in two genetic populations, viz., W82×spl-1 and PI378692×spl-1, the spotted leaf phenotype of spl-1 is controlled by a single recessive gene named lm1. The lm1 locus governing mutant phenotype of spl-1 was first identified in 3.15 Mb genomic region on chromosome 04 through MutMap analysis, which was further verified and fine mapped by simple sequence repeat (SSR) marker-based genetic mapping. Genetic linkage analysis narrowed the genomic region (lm1 locus) for mutant phenotype to a physical distance of ~76.23 kb. By searching against the Phytozome database, eight annotated candidate genes were found within the lm1 region. qRT-PCR expression analysis revealed that, among these eight genes, only Glyma.04g242300 showed highly significant expression levels in wild-type relative to the spl-1 mutant. However, sequencing data of the CDS region showed no nucleotide difference between spl-1 and its wild type within the coding regions of these genes but might be in the non-coding regions such as 5′ or 3′ UTR. Hence, the data of the present study are in favor of Glyma.04g242300 being the possible candidate genes regulating the mutant phenotype of spl-1. However, further validation is needed to prove this function of the gene as well as its role in PCD, which in turn would be helpful to understand the mechanism and pathways involved in HR disease resistance of soybean. Full article

(This article belongs to the Special Issue Legume Genetics and Biology: From Mendel's Pea to Legume Genomics)

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19 pages, 2888 KiB

Open AccessArticle

Allelic Diversity of Acetyl Coenzyme A Carboxylase accD/bccp Genes Implicated in Nuclear-Cytoplasmic Conflict in the Wild and Domesticated Pea (Pisum sp.)

by Eliška Nováková, Lenka Zablatzká, Jan Brus, Viktorie Nesrstová, Pavel Hanáček, Ruslan Kalendar, Fatima Cvrčková, Ľuboš Majeský and Petr Smýkal

Int. J. Mol. Sci. 2019, 20(7), 1773; https://doi.org/10.3390/ijms20071773 - 10 Apr 2019

Cited by 12 | Viewed by 4413

Abstract

Reproductive isolation is an important component of species differentiation. The plastid accD gene coding for the acetyl-CoA carboxylase subunit and the nuclear bccp gene coding for the biotin carboxyl carrier protein were identified as candidate genes governing nuclear-cytoplasmic incompatibility in peas. We examined [...] Read more.

Reproductive isolation is an important component of species differentiation. The plastid accD gene coding for the acetyl-CoA carboxylase subunit and the nuclear bccp gene coding for the biotin carboxyl carrier protein were identified as candidate genes governing nuclear-cytoplasmic incompatibility in peas. We examined the allelic diversity in a set of 195 geographically diverse samples of both cultivated (Pisum sativum, P. abyssinicum) and wild (P. fulvum and P. elatius) peas. Based on deduced protein sequences, we identified 34 accD and 31 bccp alleles that are partially geographically and genetically structured. The accD is highly variable due to insertions of tandem repeats. P. fulvum and P. abyssinicum have unique alleles and combinations of both genes. On the other hand, partial overlap was observed between P. sativum and P. elatius. Mapping of protein sequence polymorphisms to 3D structures revealed that most of the repeat and indel polymorphisms map to sequence regions that could not be modeled, consistent with this part of the protein being less constrained by requirements for precise folding than the enzymatically active domains. The results of this study are important not only from an evolutionary point of view but are also relevant for pea breeding when using more distant wild relatives. Full article

(This article belongs to the Special Issue Legume Genetics and Biology: From Mendel's Pea to Legume Genomics)

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Review

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30 pages, 2269 KiB

Open AccessReview

Towards Exploitation of Adaptive Traits for Climate-Resilient Smart Pulses

by Jitendra Kumar, Arbind K. Choudhary, Debjyoti Sen Gupta and Shiv Kumar

Int. J. Mol. Sci. 2019, 20(12), 2971; https://doi.org/10.3390/ijms20122971 - 18 Jun 2019

Cited by 38 | Viewed by 6993

Abstract

Pulses are the main source of protein and minerals in the vegetarian diet. These are primarily cultivated on marginal lands with few inputs in several resource-poor countries of the world, including several in South Asia. Their cultivation in resource-scarce conditions exposes them to [...] Read more.

Pulses are the main source of protein and minerals in the vegetarian diet. These are primarily cultivated on marginal lands with few inputs in several resource-poor countries of the world, including several in South Asia. Their cultivation in resource-scarce conditions exposes them to various abiotic and biotic stresses, leading to significant yield losses. Furthermore, climate change due to global warming has increased their vulnerability to emerging new insect pests and abiotic stresses that can become even more serious in the coming years. The changing climate scenario has made it more challenging to breed and develop climate-resilient smart pulses. Although pulses are climate smart, as they simultaneously adapt to and mitigate the effects of climate change, their narrow genetic diversity has always been a major constraint to their improvement for adaptability. However, existing genetic diversity still provides opportunities to exploit novel attributes for developing climate-resilient cultivars. The mining and exploitation of adaptive traits imparting tolerance/resistance to climate-smart pulses can be accelerated further by using cutting-edge approaches of biotechnology such as transgenics, genome editing, and epigenetics. This review discusses various classical and molecular approaches and strategies to exploit adaptive traits for breeding climate-smart pulses. Full article

(This article belongs to the Special Issue Legume Genetics and Biology: From Mendel's Pea to Legume Genomics)

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