scholarly journals LegumeIP V3: from models to crops—an integrative gene discovery platform for translational genomics in legumes

2020 ◽  
Vol 49 (D1) ◽  
pp. D1472-D1479
Author(s):  
Xinbin Dai ◽  
Zhaohong Zhuang ◽  
Clarissa Boschiero ◽  
Yibo Dong ◽  
Patrick X Zhao
Keyword(s):  
Agronomic Traits ◽  
Biological Data ◽  
Comparative Genomic ◽  
Biological Mechanisms ◽  
Sustainable Food ◽  
Model Legume ◽  
Translational Genomics ◽  
Legume Crops ◽  
Food And Feed ◽  
Key Genes

Abstract Legumes have contributed to human health, sustainable food and feed production worldwide for centuries. The study of model legumes has played vital roles in deciphering key genes, pathways, and networks regulating biological mechanisms and agronomic traits. Along with emerging breeding technology such as genome editing, translation of the knowledge gained from model plants to crops is in high demand. The updated database (V3) was redesigned for translational genomics targeting the discovery of novel key genes in less-studied non-model legume crops by referring to the knowledge gained in model legumes. The database contains genomic data for all 22 included species, and transcriptomic data covering thousands of RNA-seq samples mostly from model species. The rich biological data and analytic tools for gene expression and pathway analyses can be used to decipher critical genes, pathways, and networks in model legumes. The integrated comparative genomic functions further facilitate the translation of this knowledge to legume crops. Therefore, the database will be a valuable resource to identify important genes regulating specific biological mechanisms or agronomic traits in the non-model yet economically significant legume crops. LegumeIP V3 is available free to the public at https://plantgrn.noble.org/LegumeIP. Access to the database does not require login, registration, or password.

scholarly journals Identification of the Optimum Environments for the High Yield and Quality Traits of Lentil Genotypes Evaluated in Multi-Location Trials

2021 ◽  
Vol 13 (15) ◽  
pp. 8247
Author(s):  
Dimitrios N. Vlachostergios ◽  
Christos Noulas ◽  
Anastasia Kargiotidou ◽  
Dimitrios Baxevanos ◽  
Evangelia Tigka ◽  
...  
Keyword(s):  
Crude Protein ◽  
Agronomic Traits ◽  
High Yield ◽  
Breeding Programs ◽  
Growing Seasons ◽  
Yield And Quality ◽  
Food And Feed ◽  
Superior Genotypes ◽  
Selection Of ◽  
The Ideal

Lentil is a versatile and profitable pulse crop with high nutritional food and feed values. The objectives of the study were to determine suitable locations for high yield and quality in terms of production and/or breeding, and to identify promising genotypes. For this reason, five lentil genotypes were evaluated in a multi-location network consisting of ten diverse sites for two consecutive growing seasons, for seed yield (SY), other agronomic traits, crude protein (CP), cooking time (CT) and crude protein yield (CPY). A significant diversification and specialization of the locations was identified with regards to SY, CP, CT and CPY. Different locations showed optimal values for each trait. Locations E4 and E3, followed by E10, were “ideal” for SY; locations E1, E3 and E7 were ideal for high CP; and the “ideal” locations for CT were E3 and E5, followed by E2. Therefore, the scope of the cultivation determined the optimum locations for lentil cultivation. The GGE-biplot analysis revealed different discriminating abilities and representativeness among the locations for the identification of the most productive and stable genotypes. Location E3 (Orestiada, Region of Thrace) was recognized as being optimal for lentil breeding, as it was the “ideal” or close to “ideal” for the selection of superior genotypes for SY, CP, CT and CPY. Adaptable genotypes (cv. Dimitra, Samos) showed a high SY along with excellent values for CP, CT and CPY, and are suggested either for cultivation in many regions or to be exploited in breeding programs.

scholarly journals Policy Interventions Promoting Sustainable Food- and Feed-Systems: A Delphi Study of Legume Production and Consumption

2021 ◽  
Vol 13 (14) ◽  
pp. 7597
Author(s):  
Bálint Balázs ◽  
Eszter Kelemen ◽  
Tiziana Centofanti ◽  
Marta W. Vasconcelos ◽  
Pietro P. M. Iannetta
Keyword(s):  
Delphi Study ◽  
N Fertilizer ◽  
Communication Process ◽  
Smooth Transition ◽  
The European Union ◽  
Sustainable Food ◽  
Policy Interventions ◽  
Production And Consumption ◽  
Food And Feed ◽  
The Eu

The food- and feed-value systems in the European Union are not protein self-sufficient. Despite the potential of legume-supported production systems to reduce the externalities caused by current cultivation practices (excessive use of N fertilizer) and improve the sustainability of the arable cropping systems and the quality of human diets, sufficient production of high-protein legume grains in Europe has not been achieved due to multiple barriers. Identifying the barriers to the production and consumption of legumes is the first step in realizing new pathways towards more sustainable food systems of which legumes are integral part. In this study, we engage stakeholders and decision-makers in a structured communication process, the Delphi method, to identify policy interventions leveraging barriers that hinder the production and consumption of legumes in the EU. This study is one of a kind and uses a systematic method to reach a common understanding of the policy incoherencies across sectors. Through this method we identify policy interventions that may promote the production of legumes and the creation of legume-based products in the EU. Policies that encourage reduced use of inorganic N fertilizer represent an important step toward a shift in the increased cultivation of legumes. Relatedly, investment in R&D, extension services, and knowledge transfer is necessary to support a smooth transition from the heavy use of synthetic N fertilizer in conventional agriculture. These policy interventions are discussed within current EU and national plant-protein strategies.

scholarly journals Editorial: Domestication of Agronomic Traits in Legume Crops

2021 ◽  
Vol 12 ◽  
Author(s):  
Xin Chen ◽  
Gaofeng Zhou ◽  
Jiayin Pang ◽  
Peerasak Srinives
Keyword(s):  
Agronomic Traits ◽  
Legume Crops

scholarly journals Genetic Improvement of Cereals and Grain Legumes

Genes ◽  
2020 ◽  
Vol 11 (11) ◽  
pp. 1255
Author(s):  
Muhammad Amjad Nawaz ◽  
Gyuhwa Chung
Keyword(s):  
Abiotic Stresses ◽  
Genetic Improvement ◽  
Agronomic Traits ◽  
Grain Legumes ◽  
Special Issue ◽  
Biotic And Abiotic Stresses ◽  
Yield Improvement ◽  
Sustainable Food ◽  
Genetic Technologies ◽  
Global Population

The anticipated population growth by 2050 will be coupled with increased food demand. To achieve higher and sustainable food supplies in order to feed the global population by 2050, a 2.4% rise in the yield of major crops is required. The key to yield improvement is a better understanding of the genetic variation and identification of molecular markers, quantitative trait loci, genes, and pathways related to higher yields and increased tolerance to biotic and abiotic stresses. Advances in genetic technologies are enabling plant breeders and geneticists to breed crop plants with improved agronomic traits. This Special Issue is an effort to report the genetic improvements by adapting genomic techniques and genomic selection.

scholarly journals Construction of Pseudomolecules for the Chinese Chestnut (Castanea mollissima) Genome

2020 ◽  
Vol 10 (10) ◽  
pp. 3565-3574
Author(s):  
Jinping Wang ◽  
Shoule Tian ◽  
Xiaoli Sun ◽  
Xinchao Cheng ◽  
Naibin Duan ◽  
...  
Keyword(s):  
Agronomic Traits ◽  
Whole Genome Sequence ◽  
Comparative Genomic ◽  
Ecological Value ◽  
Chromosome Conformation ◽  
Protein Coding ◽  
Chinese Chestnut ◽  
Castanea Mollissima ◽  
Long Read ◽  
Improvement Programs

The Chinese chestnut (Castanea mollissima Bl.) is a woody nut crop with a high ecological value. Although many cultivars have been selected from natural seedlings, elite lines with comprehensive agronomic traits and characters remain rare. To explore genetic resources with aid of whole genome sequence will play important roles in modern breeding programs for chestnut. In this study, we generated a high-quality C. mollissima genome assembly by combining 90× Pacific Biosciences long read and 170× high-throughput chromosome conformation capture data. The assembly was 688.93 Mb in total, with a contig N50 of 2.83 Mb. Most of the assembled sequences (99.75%) were anchored onto 12 chromosomes, and 97.07% of the assemblies were accurately anchored and oriented. A total of 33,638 protein-coding genes were predicted in the C. mollissima genome. Comparative genomic and transcriptomic analyses provided insights into the genes expressed in specific tissues, as well as those associated with burr development in the Chinese chestnut. This highly contiguous assembly of the C. mollissima genome provides a valuable resource for studies aiming at identifying and characterizing agronomical-important traits, and will aid the design of breeding strategies to develop more focused, faster, and predictable improvement programs.

Comparison of genome structure between white clover and Medicago truncatula supports homoeologous group nomenclature based on conserved synteny

Genome ◽  
2008 ◽  
Vol 51 (11) ◽  
pp. 905-911 ◽  
Author(s):  
Julie George ◽  
Timothy I. Sawbridge ◽  
Noel O.I. Cogan ◽  
Anthony R. Gendall ◽  
Kevin F. Smith ◽  
...  
Keyword(s):  
Medicago Truncatula ◽  
White Clover ◽  
Agronomic Traits ◽  
Genome Structure ◽  
Draft Genome ◽  
Gene Location ◽  
Pasture Production ◽  
Model Legume ◽  
Nomenclature System ◽  
Translocation Event

Computational analysis has been used to align the genetic map of white clover ( Trifolium repens L.) with the draft genome sequence of the model legume species Medicago truncatula Gaertn. In silico comparison based on white clover expressed sequence tags that contain simple sequence repeat loci revealed substantial macrosynteny between the genomes of these two species, which are closely related within the Trifolieae tribe of the Fabaceae family. Six of the eight homoeologous chromosome groups (HGs) of allotetraploid white clover show predominant relationships with single M. truncatula (Mt) chromosomes, while the two remaining groups may have participated in an evolutionary reciprocal translocation event. On this basis, a new chromosome nomenclature system for allotetraploid white clover is proposed such that HG A = 3, HG B = 8, HG C = 7, HG D = 4, HG E = 1, HG F = 2, HG G = 5, and HG H = 6. A rationalized linkage map ordering system has also been demonstrated. Improved knowledge of the relationships between agricultural and model forage legume genomes will facilitate prediction of gene location for key agronomic traits for pasture production.

scholarly journals Increasing seed size and quality by manipulating BIG SEEDS1 in legume species

2016 ◽  
Vol 113 (44) ◽  
pp. 12414-12419 ◽  
Author(s):  
Liangfa Ge ◽  
Jianbin Yu ◽  
Hongliang Wang ◽  
Diane Luth ◽  
Guihua Bai ◽  
...  
Keyword(s):  
Seed Size ◽  
Seed Quality ◽  
Agronomic Traits ◽  
Soybean Seed ◽  
Amino Acid Content ◽  
Grain Legume ◽  
Model Legume ◽  
Plant Organs ◽  
Legume Seeds ◽  
Regulatory Module

Plant organs, such as seeds, are primary sources of food for both humans and animals. Seed size is one of the major agronomic traits that have been selected in crop plants during their domestication. Legume seeds are a major source of dietary proteins and oils. Here, we report a conserved role for the BIG SEEDS1 (BS1) gene in the control of seed size and weight in the model legume Medicago truncatula and the grain legume soybean (Glycine max). BS1 encodes a plant-specific transcription regulator and plays a key role in the control of the size of plant organs, including seeds, seed pods, and leaves, through a regulatory module that targets primary cell proliferation. Importantly, down-regulation of BS1 orthologs in soybean by an artificial microRNA significantly increased soybean seed size, weight, and amino acid content. Our results provide a strategy for the increase in yield and seed quality in legumes.

scholarly journals NUTRITIVE POTENTIAL OF SOTOL (Dasylirion cedrosanum) SEEDS

2019 ◽  
Vol 42 (4) ◽  
pp. 385-392
Author(s):  
Martha M. Orozco-Sifuentes ◽  
J. Eduardo García-Martínez ◽  
Carlos A. Arévalo-Sanmiguel ◽  
Francisca Ramírez-Godina ◽  
M. Humberto Reyes-Valdés
Keyword(s):  
Wheat Flour ◽  
Sustainable Use ◽  
Abundant Species ◽  
Arid Zones ◽  
Sustainable Food ◽  
Whole Wheat ◽  
Food And Feed ◽  
Wide Adaptation ◽  
Good Potential ◽  
Group D

Agriculture in the 21th century faces the challenge of sustainable food production in a scenario of climate change. While highly caloric processed foods increase, there is a deficiency of micronutrients, fiber and good quality protein. Sustainable use of plants with wide adaptation to harsh environments can help to improve human diet. A remarkable genus for its wide adaptation, mainly in arid lands, is Dasylirion. It comprises a group of plants commonly called sotoles, broadly distributed in arid zones of Mexico and Southern United States. The use of this wild, albeit cultivable plant, is mainly for production of an alcoholic spirit called sotol. The study of the nutritional content of Dasylirion seeds can give an added use to this genus. The purpose of this research was to assess the nutritional quality of the seeds of an abundant species of this group, D. cedrosanum. Bromatological and mineral analyses were performed in populations from the states of Coahuila and Zacatecas, in Mexico. Samples were taken from three locations, with the harvest of the seeds three plants per site and triplicate determinations with whole wheat flour control. The sotol flour had higher protein content (27.7 %), 7 times more fat (18.4 %) and 10 times more fiber (16.2 %) than wheat flour. Additionally, sotol flour had 35 times more Ca, six times more Fe and three times more Zn and Cu than wheat flour. Although these remarkable nutritional parameters were consistent across locations, the Buenavista site plants showed the highest nutritional values. These results indicate that sotol seeds have a good potential as food and feed for humans, cattle and poultry.

scholarly journals Comparative Genomic Analysis of Quantitative Trait Loci Associated With Micronutrient Contents, Grain Quality, and Agronomic Traits in Wheat (Triticum aestivum L.)

2021 ◽  
Vol 12 ◽  
Author(s):  
Nikwan Shariatipour ◽  
Bahram Heidari ◽  
Ahmad Tahmasebi ◽  
Christopher Richards
Keyword(s):  
Quantitative Trait Loci ◽  
Quantitative Trait ◽  
Grain Quality ◽  
Agronomic Traits ◽  
Meta Analysis ◽  
Crop Improvement ◽  
Comparative Genomic ◽  
Trait Loci ◽  
Stable Qtls ◽  
Improvement Programs

Comparative genomics and meta-quantitative trait loci (MQTLs) analysis are important tools for the identification of reliable and stable QTLs and functional genes controlling quantitative traits. We conducted a meta-analysis to identify the most stable QTLs for grain yield (GY), grain quality traits, and micronutrient contents in wheat. A total of 735 QTLs retrieved from 27 independent mapping populations reported in the last 13 years were used for the meta-analysis. The results showed that 449 QTLs were successfully projected onto the genetic consensus map which condensed to 100 MQTLs distributed on wheat chromosomes. This consolidation of MQTLs resulted in a three-fold reduction in the confidence interval (CI) compared with the CI for the initial QTLs. Projection of QTLs revealed that the majority of QTLs and MQTLs were in the non-telomeric regions of chromosomes. The majority of micronutrient MQTLs were located on the A and D genomes. The QTLs of thousand kernel weight (TKW) were frequently associated with QTLs for GY and grain protein content (GPC) with co-localization occurring at 55 and 63%, respectively. The co- localization of QTLs for GY and grain Fe was found to be 52% and for QTLs of grain Fe and Zn, it was found to be 66%. The genomic collinearity within Poaceae allowed us to identify 16 orthologous MQTLs (OrMQTLs) in wheat, rice, and maize. Annotation of promising candidate genes (CGs) located in the genomic intervals of the stable MQTLs indicated that several CGs (e.g., TraesCS2A02G141400, TraesCS3B02G040900, TraesCS4D02G323700, TraesCS3B02G077100, and TraesCS4D02G290900) had effects on micronutrients contents, yield, and yield-related traits. The mapping refinements leading to the identification of these CGs provide an opportunity to understand the genetic mechanisms driving quantitative variation for these traits and apply this information for crop improvement programs.

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