Legume Genetics and Biology From Mendel’s Pea to Legume Genomics Printed Edition of the Special Issue Published in International Journal of Molecular Sciences www.mdpi.com/journal/ijms Petr Smýkal, Eric J. Bishop von Wettberg and Kevin McPhee Edited by Legume Genetics and Biology Legume Genetics and Biology From Mendel’s Pea to Legume Genomics Editors Petr Sm ́ ykal Eric J. Bishop von Wettberg Kevin McPhee MDPI • Basel • Beijing • Wuhan • Barcelona • Belgrade • Manchester • Tokyo • Cluj • Tianjin Editors Petr Sm ́ ykal Palacky University Czech Republic Eric J. Bishop von Wettberg University of Vermont USA Kevin McPhee Montana State University USA Editorial Office MDPI St. Alban-Anlage 66 4052 Basel, Switzerland This is a reprint of articles from the Special Issue published online in the open access journal International Journal of Molecular Sciences (ISSN 1422-0067) (available at: https://www.mdpi.com/ journal/ijms/special issues/pea legume). For citation purposes, cite each article independently as indicated on the article page online and as indicated below: LastName, A.A.; LastName, B.B.; LastName, C.C. Article Title. Journal Name Year , Article Number , Page Range. ISBN 978-3-03936-812-9 ( H bk) ISBN 978-3-03936-813-6 (PDF) Cover image courtesy of Petr Sm ́ ykal. c © 2020 by the authors. Articles in this book are Open Access and distributed under the Creative Commons Attribution (CC BY) license, which allows users to download, copy and build upon published articles, as long as the author and publisher are properly credited, which ensures maximum dissemination and a wider impact of our publications. The book as a whole is distributed by MDPI under the terms and conditions of the Creative Commons license CC BY-NC-ND. Contents About the Editors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . vii Petr Sm ́ ykal, Eric J.B. von Wettberg and Kevin McPhee Legume Genetics and Biology: From Mendel’s Pea to Legume Genomics Reprinted from: Int. J. Mol. Sci. 2020 , 21 , 3336, doi:10.3390/ijms21093336 . . . . . . . . . . . . . . 1 Jitendra Kumar, Arbind K. Choudhary, Debjyoti Sen Gupta and Shiv Kumar Towards Exploitation of Adaptive Traits for Climate-Resilient Smart Pulses Reprinted from: Int. J. Mol. Sci. 2019 , 20 , 2971, doi:10.3390/ijms20122971 . . . . . . . . . . . . . . 7 Paolo Annicchiarico, Nelson Nazzicari, Meriem Laouar, Imane Thami-Alami, Massimo Romani and Luciano Pecetti Development and Proof-of-Concept Application of Genome-Enabled Selection for Pea Grain Yield under Severe Terminal Drought Reprinted from: Int. J. Mol. Sci. 2020 , 21 , 2414, doi:10.3390/ijms21072414 . . . . . . . . . . . . . . 37 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 Genomic Analysis of Vavilov’s Historic Chickpea Landraces Reveals Footprints of Environmental and Human Selection Reprinted from: Int. J. Mol. Sci. 2020 , 21 , 3952, doi:10.3390/ijms21113952 . . . . . . . . . . . . . . 57 Endale G. Tafesse, Krishna K. Gali, V.B. Reddy Lachagari, Rosalind Bueckert and Thomas D. Warkentin Genome-Wide Association Mapping for Heat Stress Responsive Traits in Field Pea Reprinted from: Int. J. Mol. Sci. 2020 , 21 , 2043, doi:10.3390/ijms21062043 . . . . . . . . . . . . . . 75 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 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 Reprinted from: Int. J. Mol. Sci. 2019 , 20 , 5562, doi:10.3390/ijms20225562 . . . . . . . . . . . . . . 101 Panneerselvam Krishnamurthy, Chigen Tsukamoto and Masao Ishimoto Reconstruction of the Evolutionary Histories of UGT Gene Superfamily in Legumes Clarifies the Functional Divergence of Duplicates in Specialized Metabolism Reprinted from: Int. J. Mol. Sci. 2020 , 21 , 1855, doi:10.3390/ijms21051855 . . . . . . . . . . . . . . 135 Aiman Hina, Yongce Cao, Shiyu Song, Shuguang Li, Ripa Akter Sharmin, Mahmoud A. Elattar, Javaid Akhter Bhat and Tuanjie Zhao High-Resolution Mapping in Two RIL Populations Refines Major “QTL Hotspot” Regions for Seed Size and Shape in Soybean ( Glycine max L.) Reprinted from: Int. J. Mol. Sci. 2020 , 21 , 1040, doi:10.3390/ijms21031040 . . . . . . . . . . . . . . 163 v Tengfei Zhang, Tingting Wu, Liwei Wang, Bingjun Jiang, Caixin Zhen, Shan Yuan, Wensheng Hou, Cunxiang Wu, Tianfu Han and Shi Sun A Combined Linkage and GWAS Analysis Identifies QTLs Linked to Soybean Seed Protein and Oil Content Reprinted from: Int. J. Mol. Sci. 2019 , 20 , 5915, doi:10.3390/ijms20235915 . . . . . . . . . . . . . . 199 Piotr Plewi ́ nski, Michał Ksia ̇ zkiewicz, Sandra Rychel-Bielska, El ̇ zbieta Rudy and Bogdan Wolko Candidate Domestication-Related Genes Revealed by Expression Quantitative Trait Loci Mapping of Narrow-Leafed Lupin ( Lupinus angustifolius L.) Reprinted from: Int. J. Mol. Sci. 2019 , 20 , 5670, doi:10.3390/ijms20225670 . . . . . . . . . . . . . . 219 Justyna T. Polit, Iwona Ciereszko, Alina T. Dubis, Joanna Le ́ sniewska, Anna Basa, Konrad Winnicki, Aneta ̇ Zabka, Marharyta Audzei, Łukasz Sobiech, Agnieszka Faligowska, Grzegorz Skrzypczak and Janusz Maszewski Irrigation-Induced Changes in Chemical Composition and Quality of Seeds of Yellow Lupine ( Lupinus luteus L.) Reprinted from: Int. J. Mol. Sci. 2019 , 20 , 5521, doi:10.3390/ijms20225521 . . . . . . . . . . . . . . 243 Oldˇ rich Trnˇ en ́ y, David Vlk, Eliˇ ska Mackov ́ a, Michaela Matouˇ skov ́ a, Jana ˇ Repkov ́ a, Jan Nedˇ eln ́ ık, Jan Hofbauer, Karel Vejra ˇ zka, Hana Jakeˇ sov ́ a, Jan Jansa, Lubom ́ ır Pi ́ alek and Daniela Knotova ́ Allelic Variants for Candidate Nitrogen Fixation Genes Revealed by Sequencing in Red Clover ( Trifolium pratense L.) Reprinted from: Int. J. Mol. Sci. 2019 , 20 , 5470, doi:10.3390/ijms20215470 . . . . . . . . . . . . . . 265 Paulina Glazi ́ nska, Milena Kulasek, Wojciech Glinkowski, Waldemar Wojciechowski and Jan Kosi ́ nski Integrated Analysis of Small RNA, Transcriptome and Degradome Sequencing Provides New Insights into Floral Development and Abscission in Yellow Lupine ( Lupinus luteus L.) Reprinted from: Int. J. Mol. Sci. 2019 , 20 , 5122, doi:10.3390/ijms20205122 . . . . . . . . . . . . . . 291 Suli Sun, Dong Deng, Canxing Duan, Xuxiao Zong, Dongxu Xu, Yuhua He and Zhendong Zhu Two Novel er1 Alleles Conferring Powdery Mildew ( Erysiphe pisi ) Resistance Identified in a Worldwide Collection of Pea ( Pisum sativum L.) Germplasms Reprinted from: Int. J. Mol. Sci. 2019 , 20 , 5071, doi:10.3390/ijms20205071 . . . . . . . . . . . . . . 331 G M Al Amin, Keke Kong, Ripa Akter Sharmin, Jiejie Kong, Javaid Akhter Bhat and Tuanjie Zhao Characterization and Rapid Gene-Mapping of Leaf Lesion Mimic Phenotype of spl-1 Mutant in Soybean ( Glycine max (L.) Merr.) Reprinted from: Int. J. Mol. Sci. 2019 , 20 , 2193, doi:10.3390/ijms20092193 . . . . . . . . . . . . . . 347 Eliˇ ska Nov ́ akov ́ a, Lenka Zablatzk ́ a, Jan Brus, Viktorie Nesrstov ́ a, Pavel Han ́ aˇ cek, Ruslan Kalendar, Fatima Cvrˇ ckov ́ a, ˇ Luboˇ s Majesk ́ y and Petr Sm ́ ykal Allelic Diversity of Acetyl Coenzyme A Carboxylase accD / bccp Genes Implicated in Nuclear-Cytoplasmic Conflict in the Wild and Domesticated Pea ( Pisum sp.) Reprinted from: Int. J. Mol. Sci. 2019 , 20 , 1773, doi:10.3390/ijms20071773 . . . . . . . . . . . . . . 371 vi About the Editors Petr Sm ́ ykal (Associate Professor). He received his Ph.D. in Plant Physiology and Molecular Biology at Charles University, Prague, CZ, in 1999. After 5 years of postdoctoral stays at ETH Zurich, Switzerland, and Albrecht Ludwig University of Freiburg, Germany, he then conducted research at Agritec Plant Research Ltd., Sumperk, CZ, for 10 years, working with plant genetic resources, characterizing and utilizing the genetic diversity of pea and flax germplasms. Since 2011, he has been at Department of Botany, Palacky University, in Olomouc, CZ. He is interested in study of legume seed dormancy (physical type of dormancy) and pod dehiscence, two key domestication traits, and uses a combination of anatomical, genetic, transcriptomic, and analytical chemistry tools. Seed dormancy is also studied as an adaptive trait in context of ecological genomics combining next-generation sequencing, seed testing, and geoinformatics using wild pea and Medicago truncatula models. Other favorites are crop wild relatives, particularly of legumes. Knowledge on Pisum, Cicer and Lens genus diversity is applied to broaden the respective crop genetic diversity. Eric J. Bishop von Wettberg (Associate Professor) runs a research program focused on the consequences of genetic bottlenecks limiting genetic diversity and climate resilience in crop plants. He received his Ph.D. in Ecology from Brown University in 2007 and was a NIH National Research Service Award postdoc at the University of California at Davis from 2007 to 2009. He was a faculty member at Florida International University from 2010 to 2017. Broadly trained in genetics, ecology, and agroecology, he uses a combination of field, greenhouse, common garden, and laboratory approaches to improve crop plants in the face of ongoing climate change. Many crops, like the grain legume chickpea, have lost genetic variation as a result of human cultivation and selection. The lack of genetic variation reduces resilience of these crops to expected effects of climate change. His laboratory group are using a new collection of the wild relatives of chickpea to restore genetic variation to cultivated chickpea, and to understand the genetic basis of flowering time and drought tolerance. They are also using the same approach to improve winter peas as a forage and cover crop, to improve mung beans as a summer forage and sprout crop, and to increase the disease resistance of hops. Kevin McPhee (Professor). Kevin McPhee is the Pulse Crop Breeder at Montana State University. He received his Bachelor of Science degree in Agronomy in 1991 from the University of Wyoming and his Ph.D. in Agronomy from the University of Idaho in 1995 with an emphasis on Plant Breeding and Genetics. He worked for the USDA Agricultural Research Service from 1995 to 2008, where his research focused on genetics and breeding of dry pea. From 2008 to 2016 Kevin held the position of Professor of Pulse Crop Breeding in the Department of Plant Sciences at North Dakota State University, where he conducted research on the genetics and breeding of pulse crops. In 2017, Kevin accepted the position of Professor of Pulse Crop Breeding at Montana State University. He established new pulse breeding programs at both NDSU and MSU focused on pea, lentil, and chickpea breeding for a range of research objectives. vii International Journal of Molecular Sciences Editorial Legume Genetics and Biology: From Mendel’s Pea to Legume Genomics Petr Sm ý kal 1, *, Eric J.B. von Wettberg 2 and Kevin McPhee 3 1 Department of Botany, Faculty of Sciences, Palack ý University, 779 00 Olomouc, Czech Republic 2 Department of Plant and Soil Sciences and Gund Institute for the Environment, University of Vermont, Burlington, VT 05405, USA; Eric.Bishop-Von-Wettberg@uvm.edu 3 Plant Sciences and Plant, Pathology Department, Montana State University, Bozeman, MT 59717, USA; kevin.mcphee@montana.edu * Correspondence: petr.smykal@upol.cz Received: 29 April 2020; Accepted: 6 May 2020; Published: 8 May 2020 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 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. Keywords: genomics; legumes; nitrogen fixation; proteins Introduction Legumes have always been a part of everyday life, as human food and animal feed, being key protein sources. Legumes represent the second most important family of crop plants after Poaceae (grass family), accounting for approximately 27% of the world’s crop production. While in cereals the major storage molecule is starch, which is deposited in the endosperm, in most of the grain legumes (pulses) the endosperm is transitory and consumed by the embryo during seed maturation. Legume seeds contain a high proportion of proteins (20–40%), and either lipids (soybean, peanut) or starch (or both) as a further carbon source [ 1 ]. The importance of legumes for agriculture as well as science has been recognized by the establishment of International Legume Society (ILS) in 2010 (https: // www.legumesociety.org), followed by biannual conferences bringing together people working on broad aspects of legume biology. The last ILS conference was held in 2019 in Poland and this Special Issue has been made to reflect some of the presented work. The long-term strategy of ILS is linking together the di ff erent aspects of agricultural research on grain and forage legumes worldwide. The Fabaceae is the third-largest family of flowering plants, with over 800 genera and 20,000 species. Currently, three major groups are recognized and regarded as subfamilies: the mimosoid legumes, Mimosoideae (sometimes regarded as the family Mimosaceae with four tribes and 3270 species); the papilionoid legumes, Papilionoideae (or the family Fabaceae / Papilionaceae with 28 tribes and 13,800 species); and the caesalpinioid legumes, Caesalpinoideae (or the family Caesalpiniaceae with four tribes and 2250 species) [ 2 ]. It is an extremely diverse family with a worldwide distribution, from arctic-alpine herbs to annual xerophytes and forest trees. Legumes have played an important part in cropping systems since the dawn of agriculture. Records from the oldest civilizations of Egypt and eastern Asia demonstrate the ancient use of various beans, peas, vetches, soybeans, and alfalfa. One of the early Greek botanists, Theophrastus, in the third century before Christ, wrote of leguminous plants “reinvigorating” the soil and stated that beans Int. J. Mol. Sci. 2020 , 21 , 3336; doi:10.3390 / ijms21093336 www.mdpi.com / journal / ijms 1 Int. J. Mol. Sci. 2020 , 21 , 3336 were not a burdensome crop to the ground but even seemed to manure it. The Romans emphasized the use of leguminous plants for green manuring; they also introduced the systematic use of crop rotations, a practice that was forgotten for a time during the early Middle Ages and partly also in today ́s agricultural practice. Members of the Fabaceae were domesticated as grain legumes in parallel with cereal domestications [ 3 – 8 ]. There are 13 genera (in six legume tribes) that constitute major legume crops [ 1 , 2 ]. Among the first legumes to be domesticated were members of the galegoid tribe such as peas, faba beans, lentils, grass peas and chickpeas, which arose in the Fertile Crescent of Mesopotamian agriculture. These grain legumes (pulse legumes) accompanied cereal production and formed important dietary components of early civilizations in the Near East and the Mediterranean regions. Similar domestications of Phaseolus in the New World and Glycine in East Asia have had similar importance for human dietary diversity and security. Cultivated legumes fulfill many human needs beyond being directly consumed by people. Many tree-sized species in the legume family are valuable for their hard, durable timber. Species from the genera Aeschynomene , Arachis , Centrosema , Desmodium , Macroptilium , and particularly Stylosanthes o ff er promise for improved tropical pasture systems. The barks of some species of acacias ( Acacia dealbata , A. decurrens , and A. pycnantha ) are sometimes used as sources of tannins, chemicals that are mostly used to manufacture leather from animal skins. Some important dyes are extracted from species in the legume family. One of the world’s most important natural dyes is indigo, extracted from the foliage of the indigo ( Indigofera tinctoria ) of south Asia and to a lesser degree from American indigo ( I. su ff ruticosa ) of tropical South America. Derris or rotenone is a poisonous alkaloid extracted from Derris elliptica and D. malaccensis that has long been used by indigenous peoples of Southeast Asia as arrow and fish poisons. Rotenone is now used widely as a rodenticide to kill small mammals and as an insecticide to kill pest insects. Fenugreek ( Trigonella foenum graecum ), the seeds of which are used as a spice in curries. Legumes include also valuable fiber plants, such as the sunn-hemp of India ( Crotalaria juncea ) and Hemp sesbania ( Sesbania exaltata ) used by the Indians of the southwestern United States. Some legumes such as licorice ( Glycyrrhiza glabra ) and goatsrue ( Tephrosia virginiana ) have medicinal value; many others rank among ornamental plants (for example Lathyrus odoratus ), and legumes are of great importance for honey production. The pea ( Pisum sativum L.) was the original model organism used in Mendel ́ s discovery (1866) of the laws of inheritance, making it the foundation of modern plant genetics. It had already been an object of experimental work before Mendel [ 9 , 10 ]. Despite their close phylogenetic relationships, crop legumes di ff er greatly in their genome size, base chromosome number, ploidy level, and reproductive biology. To establish a unified genetic system for legumes, two legume species in the Galegoid clade, Medicago truncatula and Lotus japonicus , from Trifolieae and Loteae tribes, respectively, were selected as model systems for studying legume genomics and biology [ 11 , 12 ]. Now, many legume crops have well-studied genetic systems. In a few cultivated legumes, comprehensive genetic analysis is limited due to the large size of their genomes. For soybeans, the most widely grown and economically important legume, a genome has been available since 2010 [ 13 ]. For the common bean ( Phaseolus vulgaris ), the most widely grown grain legume, a genome has been available since 2014 [ 14 ]. Many more legumes have been sequenced since. These genome sequences are now completed by a broad range of genomic resources, including tools for genome-wide association studies, diversity panels, and online databases [ 15 ]. These tools facilitated increasingly widespread e ff orts to implement molecular breeding in legumes. The existence of reference genomes is fundamental for the advancement of genetic mapping approaches using either classical biparental population or association mapping on wider panels. This has been shown in several papers in this issue [ 16 , 17 ] for soybean. Having genome-wide data on diversity on a su ffi ciently large and diverse set of accessions, along with accumulated phenotypic trait descriptions, provides the tools to conduct genome-wide association studies and genomic selection. This either might lead to the identification of candidate loci / genes governing studied traits or provide useful markers applicable for breeding [18,19]. 2 Int. J. Mol. Sci. 2020 , 21 , 3336 The history of legume crop domestication is not only of theoretical interest to provide insight into evolution but also can be used in breeding of recently domesticated crops, as shown in lupine [ 20 ] and potentially applied to a broader range of crop wild relatives. Legumes are particular among the plant species in their ability to fix atmospheric nitrogen. Owing to their biology including symbiotic nitrogen fixation, legumes are vital components of sustainable agriculture. This has been acknowledged in all cropping systems. Although the fundamentals of bacteria and host plant symbiosis have been elicited, there are still numerous aspects to be studied, such as allelic variation of identified genes, as shown on red clover [21]. Since most of the legume crops are used as food or feed in form of mature, dry seeds, their nutritional composition is of great importance. The study of Sivasakthi et al. [ 22 ] shows an elegant application of basic knowledge of one of the genes underlying a classical Mendelian trait, green cotyledons, identified and applied in chickpea. Seed composition can be altered by water availability or other abiotic stresses, as shown in studies of lupine seeds [ 23 ]. Similarly, dissection of the molecular mechanisms of resistance to biotic and abiotic are of high relevance both in order to understand evolutionary mechanisms between pathogens / triggers and hosts as well as to facilitate the breeding process. Mutant lines are helpful in elucidation of gene function, as shown in soybeans [ 24 ]. Since pathogens display high variation potential and are able to quickly overcome single gene / allele resistance, it is important to identify the allelic variation of a given gene, as shown in powdery mildew resistance in peas [ 25 ]. Climate change is already impacting all crops including legumes. There is a great need to understand the mechanisms of stress avoidance / tolerance / resistance to minimalize this impact. The review of Kumar et al. [ 26 ] o ff ers a view on breeding climate-resilient legume crops, which is vital particularly for tropical and subtropical countries already facing scarcity of water and soil resources. In current biology, there are commonly integrated various approaches in order to study complex biological pathways, such as that shown by the study of lupine flower development [ 27 ]. This work combines genomic, transcriptomic, and small RNA sequencing to understand the process of lupine flower ablation. Owing to progress in genomic methods such as next-generation sequencing, genetics and genomics is not limited to model species and is being applied to any species including crops with complex, polyploid genomes [ 28 ]. Evolutionary scenarios of speciation are a recurrent theme in biology, and especially in plants, there are often various pathways to speciation, including frequent hybridization and polyploidy. A central aspect of speciation is the establishment of gene-flow barriers. One of the ways to do this is the interaction between plastid and nuclear genomes leading to either viable to inviable progeny. In peas, the interaction between the chloroplast and nuclear-encoded genes results in either normal or albino / chlorotic plants. The study of Nov á kov á et al. [ 29 ] shows the variation of respective genes in natural pea populations as well as identifying the influence of a domestication-imposed bottleneck. Although Mendel’s peas were the first “model” plant, legume biology has long lagged behind more successful models from the Brassicaceae family or economically important cereals. For Borlaug, grain legumes were the “slow runners” of the green revolution because of the limited extent to which they saw the genetic gains that have characterized breeding of cereals for the past century. However, owing to progress in genomic and phenotyping technologies together with recognition of their importance for ecology of natural or agronomical systems, they are gradually gaining ground. We look for seeing new work in legumes, including releases around the world of new legume varieties bred with genomic resources. Author Contributions: E.J.B.v.W., K.M. and P.S. writing. All authors have read and agreed to the published version of the manuscript. Funding: P.S. work is supported from Grant Agency of Czech Republic and Grant Agency of Palack ý University, IGA-2020_003 project. Conflicts of Interest: The authors declare no conflict of interest. 3 Int. J. Mol. Sci. 2020 , 21 , 3336 References 1. 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Nov á kov á , E.; Zablatzk á , L.; Brus, J.; Nesrstov á , V.; Han á ˇ cek, P.; Kalendar, R.; Cvrˇ ckov á , F.; Majesk ý , L’.; Sm ý kal, P. Allelic Diversity of Acetyl Coenzyme A Carboxylase accD / bccp Genes Implicated in Nuclear-Cytoplasmic Conflict in the Wild and Domesticated Pea ( Pisum sp.). Int. J. Mol. Sci. 2019 , 20 , 1773. [CrossRef] [PubMed] © 2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http: // creativecommons.org / licenses / by / 4.0 / ). 5 International Journal of Molecular Sciences Review Towards Exploitation of Adaptive Traits for Climate-Resilient Smart Pulses Jitendra Kumar 1, *, Arbind K. Choudhary 2, *, Debjyoti Sen Gupta 1 and Shiv Kumar 3, * 1 Indian Institute of Pulses Research, Kalyanpur, Kanpur 208 024, Uttar Pradesh, India; debgpb@gmail.com 2 ICAR Research Complex for Eastern Region, Patna 800 014, Bihar, India 3 Biodiversity and Integrated Gene Management Program, International Centre for Agricultural Research in the Dry Areas (ICARDA), P.O. Box 6299, Rabat-Institute, Rabat, Morocco * Correspondence: jitendra.kumar@icar.gov.in (J.K.); akicar1968@gmail.com (A.K.C.); sk.agrawal@cgiar.org (S.K.) Received: 19 March 2019; Accepted: 28 May 2019; Published: 18 June 2019 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 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 e ff ects 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. Keywords: adaptive traits; gene / QTL; epigenetics; transgenics; genome editing; climate-smart pulses 1. Introduction Pulses are cultivated worldwide as major or minor crops (Table 1) to provide for the nutrition and livelihood of millions of peoples. Pulses, being a rich source of protein (22–26%) and micronutrients (especially Fe and Zn), are a balanced food for vegetarians when complemented with cereals. Also, the green and dry plant parts of these crops are used as feed and fodder in many livestock production systems [ 1 ], and their cultivation has long helped to sustain cereal-based cropping systems through biological nitrogen fixation and carbon sequestration [ 2 ]. Most of these pulses originated in the Mediterranean region [ 3 ]. The reproductive phase of most such crop plants often occurs in the dry climate of the Mediterranean region during spring. This favors the evolution and survival of plants with “cleistogamous” flowers, as cleistogamy prevents desiccation of anthers and stigmas and encourages full seed set by autogamy [ 4 ]. Cleistogamy of pulses appears to be a relic of evolutionary antecedents. However, such cleistogamous flower buds do open for a small period, providing opportunities for occasional natural outcrossing, which occurs in almost all pulses (including various species of cultivated Vigna ) to varying extents. This generates heterozygosity and brings about substantial heterogeneity in the population, resulting in the loss of newly developed cultivars if they go unnoticed. However, on the other hand, it makes them “resilient” to changing climate conditions, as heterozygosity in Int. J. Mol. Sci. 2019 , 20 , 2971; doi:10.3390 / ijms20122971 www.mdpi.com / journal / ijms 7 Int. J. Mol. Sci. 2019 , 20 , 2971 the population appears to confer resistance to environmental change [ 5 ]. Heterogeneity in plant populations accelerates opportunities for the selection of more stress-tolerant genotypes and thereby provides resilience to the crop as well as the ecosystem [ 6 ]. Crop plant resilience, therefore, appears to be brought about in nature by the shu ffl ing and recombination of genes at many loci, leading to the creation of novel adaptive attributes which ultimately result in enhanced “adaptedness” for a few recombinants in the changed environmental condition. Presently, the impact of global warming can be seen worldwide. For example, India has witnessed highly fluctuating weather conditions in the last decades [ 7 ]. It is evident that high temperatures have changed the rainfall pattern as well as distribution and have increased water scarcity. In the future, the shortage of water will increase drought-a ff ected regions. Moreover, it will negatively impact those regions that have higher precipitation rates [ 8 ]. The impact of climate change on chemical and physical processes in soils and nutrient uptake from soils has previously been reviewed comprehensively [ 9 ]. In Myanmar, erratic rainfall due to climate change had a detrimental impact on pulse production e ffi ciency [ 10 ]. Thus, aberrant weather conditions (global warming) are expected to pose serious threats to pulse productivity in the near future as rising temperatures will lead to production of poor biomass; reductions in days to flowering, rate of fertilization, and seed formation [ 11 – 15 ]; and intensifying vulnerability to disease and insect pests [ 1 , 16 , 17 ]. As per a Food and Agriculture Organization (FAO) report [ 18 ], climate change has put global food security more at risk; heightened the dangers of undernutrition in resource-poor regions of the world due to heat, drought, salinity, and waterlogging; and increased the threat of newly emerging diseases and insect pests. While assessing the impact of drought on crop yields, Kuwayama et al. [ 19 ] reported 0.1–1.2% yield reduction for corn and soybeans for each additional week of drought. According to Ambachew et al. [ 20 ], drought stress can cause 20–90% yield reduction in common bean, which in the worst scenario could go up to 100%. In other pulses, yield losses have been measured to the extent of 6–86% and 15–100% due to di ff erent abiotic and biotic stresses, respectively [ 21 ]. Although McKersie [ 8 ] has discussed a number of options for mitigating the e ff ects of climate change on crop production, breeding for genotypic adaptation is one of the important strategies for dealing with future climate change [ 22 ]. It involves incorporating novel traits in crop varieties to enhance food productivity and stability. For breeding climate-resilient cultivars in pulses, it is imperative to bring about genetic improvements for adaptive traits [ 22 , 23 ]. Shunmugam et al. [24] reviewed the physiological traits that may facilitate breeding climate-resilient food legume crops for adaptation under abiotic stresses. The symbiont preference traits related to abiotic stresses have recently been studied in the model legume Medicago truncatula [ 25 ]. Cullis and Kunert [ 26 ] unlocked traits that impart drought tolerance by producing a range of secondary metabolites and proteinaceous inhibitors in response to environmental stresses in orphan legume crops. As climate change is the biggest threat to the production of both warm- and cool-season pulses in the coming years, the mining of adaptive traits in the germplasm to transfer them into newly bred cultivars is highly desirable. Information on this aspect of pulse crops is still scattered in the literature. In this review, we have therefore made an attempt to organize such dispersed information and discuss various strategies to exploit adaptive traits for breeding climate-resilient smart pulses. 2. Overview of Adaptive Traits in Pulses Climate change can result in a wide range of abiotic stresses, such as drought, heat, cold, salinity, flood, and submergence, and biotic stresses, including increased attacks of pathogens and pests [ 27 ]. Therefore, breeding of adaptive traits is required for increasing the resilience of crops to current climate change conditions to help sustain productivity. Adaptive traits show their adaptive plasticity in changing environmental conditions and help crop plants survive and / or r