Cereal landraces genetic resources in worldwide GeneBanks. A review

Since the dawn of agriculture, cereal landraces have been the staples for food production worldwide, but their use dramatically declined in the 2nd half of the last century, replaced by modern cultivars. In most parts of the world, landraces are one of the most threatened components of agrobiodiversity, facing the risk of genetic erosion and extinction. Since landraces have a tremendous potential in the development of new cultivars adapted to changing environmental conditions, GeneBanks holding their genetic resources potentially play an important role in supporting sustainable agriculture. This work reviews the current knowledge on cereal landraces maintained in GeneBanks and highlights the strengths and weaknesses of existing information about their taxonomy, origin, structure, threats, sampling methodologies and conservation and GeneBanks’ documentation and management. An overview of major collections of cereal landraces is presented, using the information available in global metadatabase systems. This review on winter cereal landrace conservation focuses on: (1) traditional role of GeneBanks is evolving beyond their original purpose to conserve plant materials for breeding programmes. Today’s GeneBank users are interested in landraces’ history, agro-ecology and traditional knowledge associated with their use, in addition to germplasm traits. (2) GeneBanks therefore need to actively share their germplasm collections’ information using different channels, to promote unlimited and effective use of these materials for the further development of sustainable agriculture. (3) Access to information on the 7.4 million accessions conserved in GeneBanks worldwide, of which cereal accessions account for nearly 45 %, particularly information on cereal landraces (24 % of wheat, 23 % of barley, 14 % of oats and 29 % of rye accessions), is often not easily available to potential users, mainly due to the lack of consistent or compatible documentation systems, their structure and registration. (4) Enhancing the sustainable use of landraces maintained in germplasm collections through the effective application of recent advances in landrace knowledge (origin, structure and traits) and documentation using the internet tools and data providing networks, including the use of molecular and biotechnological tools for the material screening and detection of agronomic traits. (5) Cereal landraces cannot be exclusively conserved as seed samples maintained under ex situ conditions in GeneBanks. The enormous contribution of farmers in maintaining the crop and landraces diversity is recognised. Sharing of benefits and raising awareness of the value of cereal landraces are the most effective ways to promote their conservation and to ensure their continued availability and sustainable use. (6) Evaluation of costs and economic benefits attributed to sustainable use of cereal landraces conserved in the GeneBanks requires comprehensive studies conducted on a case-by-case basis, that take into consideration species/crop resources, conservation conditions and quality and GeneBank location and functions.This work was support by the European Community, through the INTERREG IIIB and MAC programmes, research projects Germobanco Agrícola da Macaronesia and AGRICOMAC. This paper was edited by Olga Spellman (Bioversity International)info:eu-repo/semantics/publishedVersio

Plant Germplasm Resources

Landraces and wild relatives of crops from centers of diversity have been rich sources of resistance to new pathogens, insect pests, and other stresses as well as for traits to improve food and fiber quality, animal feed, and industrial products. Because very few crops grown in the U.S. are native, plant introductions are vital to our agriculture. The National Plant Germplasm System (NPGS) was established to acquire, preserve, and distribute plant genetic resources from around the world so that scientists have immediate access to these source materials. The active collection is maintained and distributed by 19 national germplasm repositories. The base collection is preserved at -I8°C at the National Seed Storage Laboratory. The NPGS\u27s genetic resources are made freely available to all bona fide users for the benefit of humankind. Recent international agreements such as the Biodiversity Convention will impact acquisition and exchange of germplasm, but the NPGS goal is to maintain the germplasm exchange critical to feeding the increasing world population in the future

Exploiting genetic and genomic resources to enhance productivity and abiotic stress adaptation of underutilized pulses

Underutilized pulses and their wild relatives are typically stress tolerant and their seeds are packed with protein, fibers, minerals, vitamins, and phytochemicals. The consumption of such nutritionally dense legumes together with cereal-based food may promote global food and nutritional security. However, such species are deficient in a few or several desirable domestication traits thereby reducing their agronomic value, requiring further genetic enhancement for developing productive, nutritionally dense, and climate resilient cultivars. This review article considers 13 underutilized pulses and focuses on their germplasm holdings, diversity, crop-wild-crop gene flow, genome sequencing, syntenic relationships, the potential for breeding and transgenic manipulation, and the genetics of agronomic and stress tolerance traits. Recent progress has shown the potential for crop improvement and food security, for example, the genetic basis of stem determinacy and fragrance in moth bean and rice bean, multiple abiotic stress tolerant traits in horse gram and tepary bean, bruchid resistance in lima bean, low neurotoxin in grass pea, and photoperiod induced flowering and anthocyanin accumulation in adzuki bean have been investigated. Advances in introgression breeding to develop elite genetic stocks of grass pea with low β-ODAP (neurotoxin compound), resistance to Mungbean yellow mosaic India virus in black gram using rice bean, and abiotic stress adaptation in common bean, using genes from tepary bean have been carried out. This highlights their potential in wider breeding programs to introduce such traits in locally adapted cultivars. The potential of de-domestication or feralization in the evolution of new variants in these crops are also highlighted

Germplasm evaluation for crop improvement: Analysis of grain quality and cadmium accumulation in barley

Evaluating genetic variation in barley (Hordeum vulgare) germplasm, combined with genome-wide genotyping, is vital for identifying genes controlling important grain-quality traits. For example, in addition to traditional grain quality properties such as starch and protein contents, grain safety parameters such as heavy metal content, are important in the use of barley for human food and animal feed. A number of genes affecting grain quality have been identified by map-based cloning strategies and functionally analyzed by genetic transformation experiments. Moreover, germplasm evaluation yielded information that enabled the introgression of a key gene controlling grain cadmium accumulation into an elite barley cultivar, reducing the content of this heavy metal in grain. Genotyping of molecular markers and resequencing of germplasm accessions may provide information about how grain quality–related loci evolved and how the current allelic diversity was established. In this review, we describe germplasm resources for barley grain quality–related traits and the methods used to analyze the functions of genes controlling these traits, illustrating cadmium accumulation as an example. We also discuss future directions for the efficient identification of grain quality–related genes.Evaluating genetic variation in barley (Hordeum vulgare) germplasm, combined with genome-wide genotyping, is vital for identifying genes controlling important grain-quality traits. For example, in addition..

Genetic Diversity among Cowpea (Vigna unguiculata (L.) Walp.) Landraces Suggests Central Mozambique as an Important Hotspot of Variation

Cowpea is a multiple-purpose drought-tolerant leguminous pulse crop grown in several dry tropical areas. Its domestication center is thought to be East or West Africa, where a high level of genetic diversity is apparently still found. However, detailed genetic information is lacking in many African countries, limiting the success of breeding programs. In this work, we assessed the genetic variation and gene flow in 59 Vigna unguiculata (cowpea) accessions from 10 landraces spanning across six agro-ecological zones of Mozambique, based on nuclear microsatellite markers. The results revealed the existence of high genetic diversity between the landraces, even in comparison to other world regions. Four genetic groups were found, with no specific geographic pattern, suggesting the presence of gene flow between landraces. In comparison, the two commercial varieties had lower values of genetic diversity, although still close to the ones found in local landraces. The high genetic diversity found in Mozambique sustains the importance of local genetic resources and farm protection to enhance genetic diversity in modern varieties of cowpea worldwide.This research received funds from the Mozambican Fundo Nacional de Investigação (Project 201-Inv-FNI), NUFFIC, the Netherlands (Project NICHE-Moz-151), and Fundação para a Ciência e a Tecnologia, I.P., through the Ph.D. fellowship SFRH/BD/113952/2015 (A.M.F.G.) and the post-doctoral fellowship SFRH/BPD/100384/2014 (D.D), the research units UID/04129/2020 (LEAF), UIDP/04035/2020 (GeoBioTec), and UIDB/00239/2020 (CEF), and the APC.info:eu-repo/semantics/publishedVersio

에티오피아 고추의 유전적 다양성 분석 및 고추에서의 Up 유전자 연관 유전자지도 작성

학위논문(박사)--서울대학교 대학원 :농업생명과학대학 원예학과,2020. 2. Kang, Byoung Cheorl .에티오피아 유전자 은행에 보존된 고추 유전자원의 다양성 연구와 고추 과실의 기원을 조절하는 유전적 요인들을 이해하는 것은 육종에 중요한 정보를 제공할 수 있다. 작물 유전자원의 다양성의 구조와 깊이를 연구하는 것은 이용가능 한 유전적 자원의 실용화와 보존에 매우 필수적이다. 에티오피아에서 고추는 매우 경제적이고 사회적 중요성을 가진 작물임에도 불구하고, 단일염기다형성(SNP) 마커를 이용한 유전적 다양성에 관련한 자세한 연구는 제한적이다. 따라서, 에티오피아 고추 유전자원의 다양성과 유전적 구조를 조사하기 위해, 에티오피아 생물다양성 연구소에서 수집하고 유지된 총 142 종에 대하여 평가하였다. 우리는 53,284 genome wide SNP 분자마커를 genotyping-by-sequencing (GBS)를 이용하여 발견하여 검증하였다. 우리는 모델 기반의 집단 구조, 계통도, 주성분 분석을 사용하여 C. annuum 과 C. frutescens를 각각 132종과 9종의 두 개의 뚜렷한 집단으로 확인하였다. 이 밖에도, 전장유전체 연관 분석 (GWAS) 결과로 과실, 줄기, 잎 관련 특성과 크게 연관된 509개의 SNP 마커를 발견하였다. 전반적으로, 이 연구는 보존과 육종이라는 관점에서 에티오피아 고추 종에 존재하는 유전적 다양성을 이해하는데 유용할 것이다. 고추의 과실방향에서 두개의 주요한 시장으로, pendant와 upright가 있다. 과실의 Pendant 와 upright 방향 그리고 드물게 발생하는 중간형은 집단의 구조에 따라 과실이 달리기 전과 후에 쉽게 구별되어지는 형태학적 가변성을 판별하는 것이다. 고추 핵심 집단 (core collection)에서 GWAS 분석을 통한 highly significant SNP와 3개의 양친형 집단 (bi-parental population)으로부터 유전자를 발견하는 것은 염색체 7번에 존재하는 과실의 방향성을 조절하는 유전자좌의 맵핑 구역을 좁혀가는 것을 가능하게 한다. 추가로 분자 마커를 개발하고, 과실 방향에 기초하는 후보 유전자를 분리하기 위해, Capsicum annuum LA F2 mapping population 을 사용하여 fine mapping을 수행하였다. 450 individuals로 구성된 LA F2 mapping population은 양친형 라인인 C. annuum LP97 and A79의 교배를 통해 개발되었다. 유전자 분석 결과 상향 과실 방향의 포현형은 단일 열성 유전자 Up에 의하여 조절됨을 나타냈다. Up 유전자좌의 fine mapping을 위해 150개의 SNP 분자마커가 사용되었다. 유전자 분석 결과 상향 과실 방향의 포현형은 단일 열성 유전자 Up에 의하여 조절됨을 나타냈다. Up 유전자좌의 fine mapping을 위해 150개의 SNP 분자마커가 사용되었다. 이 두개의 마커 서열은CM334 유전체에 정렬되었으며, Up 유전자좌는 101kb genomic region으로 구분되었다. 대상 지역에서 13개의 후보유전자가 예측되었다. 후보유전자의 CDS 영역인 Zinc finger MYM-type protein 1-like는 66과 75 위치의 두 개의 비 동의 염기치환과, 첫번째 뉴클레오타이드의 104bp 에서 104b에서 한 개의 염기 결실을 나타내었다. 이러한 돌연변이는 12개의 parental line과 5개의 종에서 일관되게 관찰되었다. 따라서 이 유전자는 Up 유전자좌에 매우 유력한 후보유전자였다. 이 연구를 통해 얻은 정보는 분자표지 기반 선발을 통하여 조기 과실 방향 결정으로 고추 품종의 특성과 육종에 대한 추가 연구를 촉진할 것이다.Diversity study of Capsicum germplasms preserved in the Ethiopian Gene bank and understanding genetic factors that controls the fruit orientation in pepper can provide important information for breeding. Investigating the extent and structure of crop germplasm diversity is essential for the conservation and utilization of the available genetic resources. Despite the great economic and social importance of pepper in Ethiopia, detailed studies of the genetic diversity using single nucleotide polymorphism (SNP) markers is limited. Thus, with the objective of investigating the variability and genetic structure of Ethiopian pepper germplasms, a total of 142 accessions which were collected and maintained by the Ethiopian Biodiversity Institute were evaluated. We identified and validated 53,284 genome wide SNP molecular markers using genotyping-by-sequencing (GBS). Employing model based population structure, phylogenetic tree and principal coordinate analysis, we identified C. annuum and C. frutescens as two distinct genetic populations with 132 and 9 accessions, respectively. Besides this, genome wide association (GWAS) analysis detected 509 SNP markers that were significantly associated with fruit, stem and leaf-related traits. Overall, this report is useful to understand the genetic variability existed in Ethiopian Capsicum species, for its conservation and breeding. There are specific known markets for the two major fruit orientation in pepper, i.e. pendant and upright. Pendant and upright position with rare occurrence of intermediate orientation of pepper fruit is a distinguishing morphological variability that can be easily recognized before or after the fruit is set, depending on the population types. Identification of genes from three different bi-parental populations and highly significant SNP positions from GWAS analysis of Capsicum core collection enable us to narrow down the mapping region of fruit orientation controlling the locus in chromosome 12. To further develop molecular markers and isolate the candidate gene underlying fruit orientation, fine mapping was performed using Capsicum annuum LA F2 mapping population. The LA F2 mapping population consisting of 450 individuals was developed from the cross between parental lines C. annuum LP97 and A79. Genetic analysis revealed that the phenotype of the up fruit orientation was controlled by a single recessive gene, Up. One hundred fifty SNP markers were used for fine mapping of the Up locus. High-resolution genetic mapping of these markers in Karia F2 mapping population placed Redu0119 and SAR201-1386 at genetic distances of 0.8 and 0.6 cM, respectively, on either side of the Up locus. These two marker sequences were aligned to the CM334 genome and the Up locus was delimited to a 101 kb genomic region. Fifteen candidate genes were predicted in the target region. Overall, there were a total of 31 conservative amino acid substitutions, due to 18 non-synonymous and 13 synonymous nucleotide switches. The first CDS region of the candidate gene, Zinc finger MYM-type protein 1-like has displayed one non-synonymous nucleotide substitution at 106 bp and one nucleotide deletion at 104 bp. Therefore, Zinc finger MYM-type protein 1-like was the most likely candidate gene for the Up locus. The information obtained here will facilitate further research on the trait and breeding of pepper varieties with the early determination of fruit orientation through marker-assisted selection.GENERAL INTRODUCTION 1 CHAPTER I Genetic Diversity of Ethiopian Capsicum spp 12 ABSTRACT 13 INTRODUCTION 15 MATERIALS AND METHODS 20 Plant materials 20 Morphological characterization and statistical analysis 23 DNA extraction and library construction for genotyping by sequencing 24 HRM-PCR amplification and data analysis 25 Sequencing data analysis, SNP identification and genome-wide association analysis 28 Genetic diversity and population structure analysis 29 Phylogenetic and principal-coordinate analyses 30 RESULTS 31 Species identification based on HRM genotyping 31 Qualitative and quantitative morphological characterization 33 GBS and single-nucleotide polymorphisms 41 Genetic diversity 44 Analysis of molecular variance 46 Population structure 48 Molecular phylogenetic and principal-coordinate analysis 50 GWAS for selected traits 52 DISCUSSION 61 REFERENCES 67 CHAPTER II Fine mapping of the Up gene controlling fruit orientation in pepper (Capsicum spp.) 76 ABSTRACT 77 INTRODUCTION 79 MATERIALS AND METHODS 82 Plant materials 82 Growing conditions and phenotyping 82 Light microscopic observation 83 Genomic DNA extraction 83 Genotyping-by-sequencing 84 Development of SNP markers and linkage analysis of molecular markers 84 PCR amplification and localization of the Up gene 86 Gene cloning and sequencing 87 RESULTS 89 Fruit orientation in pepper and its temporal change 89 Pedicel morphology in segregation population and its correlation with other related traits 90 Inheritance analysis of fruit position 91 Localization of the target region for Up locus 100 Fine-mapping of Up locus and validation of markers 107 Confirmation of sequence variations in candidate genes 113 Phylogenic analysis 122 DISCUSSION 124 REFERENCES 130 ABSTRACT IN KOREAN 137Docto

Genome-wide association mapping of zinc and iron concentration in barley landraces from Ethiopia and Eritrea

Mamo, B.E., Barber, B., Steffenson, B.J., 2014. Genome- wide association mapping of zinc and iron concentration in barley landraces from Ethiopia and Eritrea. J. Cereal Sci. XX, XX-XX.Barley is one of the oldest cultivated crop plants and is a major part of a staple diet in some developing countries. The objectives of this study were to characterize genetic variation in grain zinc and iron concentration and kernel weight, and identify quantitative trait loci (QTL) associated with these traits in barley landraces from Ethiopia/Eritrea using a genome-wide association study (GWAS). Barley landraces were grown under greenhouse and field conditions, characterized for micronutrient concentration and kernel weight, and then genotyped with 7842 single nucleotide polymorphism (SNP) markers. The germplasm exhibited a wide range of variation for these traits with some accessions having high levels of zinc and iron. Heritability values of 0.65 and 0.59, respectively, were obtained for zinc and iron concentrations in grain samples harvested from field trials. One QTL associated with grain zinc concentration was identified in a unique genomic location on the long arm of chromosome 6H. For kernel weight, a known QTL region on the long arm of chromosome 2H was detected. This study demonstrates the existence of high genetic variation for grain zinc and iron concentration in Ethiopian/Eritrean barley landraces and also the utility of GWAS for identifying and mapping QTL underlying micronutrient accumulation

Reap the crop wild relatives for breeding future crops

Crop wild relatives (CWRs) have provided breeders with several 'game-changing' traits or genes that have boosted crop resilience and global agricultural production. Advances in breeding and genomics have accelerated the identification of valuable CWRs for use in crop improvement. The enhanced genetic diversity of breeding pools carrying optimum combinations of favorable alleles for targeted crop-growing regions is crucial to sustain genetic gain. In parallel, growing sequence information on wild genomes in combination with precise gene-editing tools provide a fast-track route to transform CWRs into ideal future crops. Data-informed germplasm collection and management strategies together with adequate policy support will be equally important to improve access to CWRs and their sustainable use to meet food and nutrition security targets