Genetic Diversity Of Landraces Research Articles

A diverse panel of 755 bread wheat accessions harbors untapped genetic diversity in landraces and reveals novel genetic regions conferring powdery mildew resistance

Key message A bread wheat panel reveals rich genetic diversity in Turkish, Pakistani and Iranian landraces and novel resistance loci to diverse powdery mildew isolates via subsetting approaches in association studies.Wheat breeding for disease resistance relies on the availability and use of diverse genetic resources. More than 800,000 wheat accessions are globally conserved in gene banks, but they are mostly uncharacterized for the presence of resistance genes and their potential for agriculture. Based on the selective reduction of previously assembled collections for allele mining for disease resistance, we assembled a trait-customized panel of 755 geographically diverse bread wheat accessions with a focus on landraces, called the LandracePLUS panel. Population structure analysis of this panel based on the TaBW35K SNP array revealed an increased genetic diversity compared to 632 landraces genotyped in an earlier study and 17 high-quality sequenced wheat accessions. The additional genetic diversity found here mostly originated from Turkish, Iranian and Pakistani landraces. We characterized the LandracePLUS panel for resistance to ten diverse isolates of the fungal pathogen powdery mildew. Performing genome-wide association studies and dividing the panel further by a targeted subsetting approach for accessions of distinct geographical origin, we detected several known and already cloned genes, including the Pm2a gene. In addition, we identified 22 putatively novel powdery mildew resistance loci that represent useful sources for resistance breeding and for research on the mildew-wheat pathosystem. Our study shows the value of assembling trait-customized collections and utilizing a diverse range of pathogen races to detect novel loci. It further highlights the importance of integrating landraces of different geographical origins into future diversity studies.

SELECTION OF SUPERIOR GENOTYPES OF LIMA BEAN LANDRACES BY MULTIVARIATE APPROACH

ABSTRACT The knowledge of genetic diversity in plant population is essential to the success of plant breeding programs. Thus, previous characterization of landraces is one of the first steps before the indication of genotypes to these plant breeding programs. This study aimed to characterize, through morphological traits, and estimate the genetic diversity in landraces of lima bean (Phaseolus lunatus L.). Genetic diversity was estimated by using multivariate methods that selected individual landraces to be indicated for farmers and consumers. According to morphological traits proposed by Biodiversity International, the genotypes UFPI-667 and UFPI- 682 showed higher dissimilarity and high potential to be used in crosses since they are genetically distant and complementary. The principal component analysis identified positive and significant phenotypic associations between variables: pod length, pod width, and grain production. According to the multivariate methods used, the landraces UFPI-666, UFPI-650, UFPI-651, UFPI-687, UFPI-658, UFPI-673, UFPI-667, and UFPI-674 are potential candidates for selection since they have relevant features for lima bean breeding, such as shorter cycles and higher grain production. This study showed that multivariate analysis can be used as an effective tool to find potential traits in lima bean and can assist the lima bean breeders in the selection of potential landraces. Accessions UFPI-667 and UFPI-682 can be indicated as genitors for breeding programs, as they are genetically distant and complementary in their characteristics.

Genetic Diversity of Landraces and Improved Varieties of Rice (Oryza sativa L.) in Taiwan

BackgroundRice, the most important crop in Asia, has been cultivated in Taiwan for more than 5000 years. The landraces preserved by indigenous peoples and brought by immigrants from China hundreds of years ago exhibit large variation in morphology, implying that they comprise rich genetic resources. Breeding goals according to the preferences of farmers, consumers and government policies also alter gene pools and genetic diversity of improved varieties. To unveil how genetic diversity is affected by natural, farmers’, and breeders’ selections is crucial for germplasm conservation and crop improvement.ResultsA diversity panel of 148 rice accessions, including 47 cultivars and 59 landraces from Taiwan and 42 accessions from other countries, were genotyped by using 75 molecular markers that revealed an average of 12.7 alleles per locus with mean polymorphism information content of 0.72. These accessions could be grouped into five subpopulations corresponding to wild rice, japonica landraces, indica landraces, indica cultivars, and japonica cultivars. The genetic diversity within subpopulations was: wild rices > landraces > cultivars; and indica rice > japonica rice. Despite having less variation among cultivars, japonica landraces had greater genetic variation than indica landraces because the majority of Taiwanese japonica landraces preserved by indigenous peoples were classified as tropical japonica. Two major clusters of indica landraces were formed by phylogenetic analysis, in accordance with immigration from two origins. Genetic erosion had occurred in later japonica varieties due to a narrow selection of germplasm being incorporated into breeding programs for premium grain quality. Genetic differentiation between early and late cultivars was significant in japonica (FST = 0.3751) but not in indica (FST = 0.0045), indicating effects of different breeding goals on modern germplasm. Indigenous landraces with unique intermediate and admixed genetic backgrounds were untapped, representing valuable resources for rice breeding.ConclusionsThe genetic diversity of improved rice varieties has been substantially shaped by breeding goals, leading to differentiation between indica and japonica cultivars. Taiwanese landraces with different origins possess various and unique genetic backgrounds. Taiwanese rice germplasm provides diverse genetic variation for association mapping to unveil useful genes and is a precious genetic reservoir for rice improvement.

Do the importations of crop products affect the genetic diversity from landraces? A study case in garlic (Allium sativum L.)

The increase in importations of elite garlic (Allium sativum L.) in Brazil to meet the local demand in many cities may affect the cultivation of garlic landraces in small family farming systems by driving to the reduction of the harvested area and genetic diversity. The landraces are fundamental sources of genetic variability and adapted germplasm that could be potentially be implemented in breeding programs. The objective of this study was to evaluate the changes in the patterns of genetic diversity in landraces cultivated in family farming systems after three decades of competitiveness with imported garlic. Three landraces of garlic currently cultivated on family farms in the Picos municipality and immediate regions (7° 04′ 55.5″ S 41° 28′ 04.2″ W) and a landrace collected in the same region in the 1970s, before the increase of imports of garlic in Brazil, were selected for this study. Additionally, six garlic accessions from the Garlic Germplasm Bank from ESALQ/USP (Sao Paulo—Brazil) were selected to parallel the genetic diversity present in landraces with other varieties collected in Brazil, completing a set of ten accessions. A randomized block design was used to evaluate nine agro-morphological traits and rank the landraces according to the economically important agronomic traits. The potential changes in genetic diversity patterns and population structure in these populations were also evaluated at a molecular level using eight microsatellite markers. The agro-morphological evaluation indicates that there is genetic diversity in the garlic populations, and it is structured between Picos landraces and ESALQ/USP accessions. There is also evidence of genetic structure between the landraces and populations of the ESALQ/USP accessions (K = 3) based on a Bayesian clustering approach. The moderate genetic differentiation (FST = 0.09) accessed by the microsatellite markers may be associated with the existence of these two different gene pools: Picos landraces and ESALQ/USP accessions. The results indicate that the reduction in harvested areas in the past decades did not affect most morphological characteristics in the landraces, but there was a reduction in the quality of the bulbs. The garlic landraces cultivated nowadays in Picos municipality present a higher number of cloves per bulb, an undesirable characteristic that may affect its commercial value. However, we demonstrate that even with such reduction in harvested areas due to the lack of competitiveness of landraces, there was no reduction in the molecular genetic diversity in these landraces accessed by the microsatellite markers. These are promising results since there is genetic diversity to implement these landraces in genetic breeding programs.

Enset in Ethiopia: a poorly characterized but resilient starch staple.

Enset (Ensete ventricosum, Musaceae) is an African crop that currently provides the staple food for approx. 20 million Ethiopians. Whilst wild enset grows over much of East and Southern Africa and the genus extends across Asia to China, it has only ever been domesticated in the Ethiopian Highlands. Here, smallholder farmers cultivate hundreds of landraces across diverse climatic and agroecological systems. Enset has several important food security traits. It grows over a relatively wide range of conditions, is somewhat drought-tolerant, and can be harvested at any time of the year, over several years. It provides an important dietary starch source, as well as fibres, medicines, animal fodder, roofing and packaging. It stabilizes soils and microclimates and has significant cultural importance. In contrast to the other cultivated species in the family Musaceae (banana), enset has received relatively little research attention. Here, we review and critically evaluate existing research, outline available genomic and germplasm resources, aspects of pathology, and explore avenues for crop development. Enset is an underexploited starch crop with significant potential in Ethiopia and beyond. Research is lacking in several key areas: empirical studies on the efficacy of current agronomic practices, the genetic diversity of landraces, approaches to systematic breeding, characterization of existing and emerging diseases, adaptability to new ranges and land-use change, the projected impact of climate change, conservation of crop wild relatives, by-products or co-products or non-starch uses, and the enset microbiome. We also highlight the limited availability of enset germplasm in living collections and seedbanks, and the lack of knowledge of reproductive and germination biology needed to underpin future breeding. By reviewing the current state of the art in enset research and identifying gaps and opportunities, we hope to catalyse the development and sustainable exploitation of this neglected starch crop.

Molecular Genetic Diversity of Landraces, Cultivars and Wild Relatives of Rice of Goa

We studied 51 rice varieties to understand their genetic diversity. Out of 19 ISSR primers, 15 primers produced reproducible bands. Out of 110 ISSR bands, 104 were polymorphic bands with an average of 6.93 bands per primer. The amount of polymorphism varied from 50% to 100%, with an average of 92%. Genetic identity value ranged from 0.5091 to 0.9727, with an average of 0.740. Dendrogram revealed the formation of four major clusters. Wild rice Oryza rufipogon formed a separate clade, indicating its uniqueness. Our study opens up avenues for use of traditional rice varieties for rice breeding, genome-wide association mapping and conservation of rice germplasm.

Genetic diversity in the rice landraces (Oryza sativa L.) of coastal Sundarbans (India) and their adaptation to the local saline condition investigated both at molecular and physiological level

Salinity is one of the major impediments to increase production in rice growing areas worldwide as the crop is sensitive to saline conditions. The key to breed new rice varieties depends on utilization of genetic diversity in landraces that possess many useful genes/alleles. The diversity present among the fifty rice accessions, collected from 4 geographical areas of Sundarbans, India, an area well known for its genetic diversity, was analysed at the genomic level by employing hyper variable microsatellite markers. As these accessions are well adapted to saline conditions, haplotype analysis conducted on Saltol locus, which has four genes that are known to confer salinity in rice, could identify eight different haplotypes. Wide variation was also seen for Na+/K+ ratio among the accessions and an association was detected between markers RM8094, RM3412 and RM493 and Na+/K+ ratio of rice plants under salinity stress. Based on the morphological, physiological and molecular analyses, Nonabokra, Kumrogoor and Kalonunia were identified as potential donors as the tolerance in these genotypes appear to be regulated by alleles other than the ones present in FL478, a well-known donor for salinity in rice.

Assessing Genetic Diversity in Landraces of Cucurbita spp. Using a Morphological and Molecular Approaches

Agriculture can only be considered as sustainable if it includes a suitable system of plant genetic resources conservation. Crop genetic resources conservation is an insurance against risks to food security. The landraces stand important genetic resources for plant breeders due to its genotypic variability. In Portugal, the production of Cucurbita is based in old local cultivars and is mainly for self-consumption (human food or feed) and is sale on local markets. To evaluate the diversity of 54C. pepo, 32C. maxima and 21C. moschata populations collected in Northern and inner center of Portugal, 20 morphological traits from the Minimum Descriptors for Cucurbita spp. and six microsatellites were used. The traits that registered the highest mean values were the fruit length, the skin thickness and the seed weight, in C. pepo, the fruit width and 100 seed weight in C. maxima and the fruit weight and flesh thickness in C. moschata populations. The ANOVA revealed significant differences (P<0.05) for all traits, with exception of skin thickness parameter. The PCA showed that the three most informative PC explained 52.5% of the total variation and a clear separation of the three species. The molecular analysis with SSR markers revealed a polymorphism of 100%. The Ho and He average were 0.316 and 0.447, respectively. The PIC showed an average of 0.688. The hierarchical analysis revealed a clear separation of the three Curcubita species. The PCoA showed that the three most informative PC explained 66.3% of the total variation and clearly separated the three species studied. The high genetic diversity found in this Portuguese collection of Cucurbita spp. provides relevant information for the diversity conservation and can be useful for breeding programs.

Potential loss of unique genetic diversity in tomato landraces by genetic colonization of modern cultivars at a non‐center of origin

AbstractWe report the genetic diversity of tomato landraces from Myanmar, with reference to worldwide tomato accessions. Ten simple sequence repeat markers were screened and used to create diversity profiles of tomato germplasm. A total of 133 alleles were amplified from the germplasm investigated; alleles specific to landraces from Myanmar were also observed. Higher genetic diversity for the Myanmar landraces highlighted the broad genetic base of tomato germplasm. Principal component analysis showed that most of the Myanmar landraces were divergent from other accessions. The different approaches used to analyse landrace diversity documented the broader genetic base of germplasm from Myanmar, which is a non‐center of origin for tomato. Genetic diversity in the landraces may be attributable to diverse production systems used by different ethnic groups in Myanmar, ranging from natural hydroponics in eastern areas, to slash‐and‐burn fields in mountain areas and shifting cultivation in many parts of the country. The availability of uniform and high‐yielding cultivars/hybrids threatens the valuable landraces in Myanmar. We emphasize the need to evaluate tomato germplasm from Myanmar for different traits and sustainable use with simultaneous conservation.

Role of seed flow on the pattern and dynamics of pearl millet (Pennisetum glaucum [L.] R. Br.) genetic diversity assessed by AFLP markers: a study in south-western Niger

We studied the regional genetic diversity and seed exchange dynamics of pearl millet landraces in south-western Niger. The genetic study was based on AFLP markers. We found significant genetic differentiation between landraces in different geographical areas of south-western Niger. However, the degree of differentiation was low insofar as only 1.9% of the total molecular diversity was due to regional differentiation, suggesting a relatively high gene flow. Anthropologic studies on farming practices have suggested that seed exchanges between farmers on a large geographical scale probably make a considerable contribution to this result. In order to test this hypothesis, the effects of seed exchange on the genetic diversity of landraces was analyzed on seed samples from two distant villages in contrasting areas of south-western Niger. Seeds imported by farmers into the southern village of Sina Koara did not differ significantly from locally grown landraces. By contrast, in the northern village of Alzou, several samples were genetically different from locally grown landraces and closer to southern accessions. These data suggest that the seed flow is preferentially from south to north, i.e. from an area with more favorable rainfall conditions. The potential consequences for the genetic diversity and adaptation of northern pearl millet landraces are discussed.

Genetic Diversity of Landraces in Gossypium arboreum L. Race sinense Assessed with Simple Sequence Repeat Markers

AbstractAsiatic cotton (Gossypium arboreum L.) is an “Old World” cultivated cotton species, the sinense race of which is planted extensively in China. This species is still used in the current tetraploid cotton breeding program as an elite germplasm line, and is also used as a model for genomic research in Gossypium. In the present study, 60 cotton microsatellite markers, averaging 4.6 markers for each A‐genome chromosome, were chosen to assess the genetic diversity of 109 accessions. These included 106 G. arboreum landraces, collected from 18 provinces throughout four Asiatic cotton‐growing regions in China. A total of 128 alleles were detected, with an average of 2.13 alleles per locus. The largest number of alleles, as well as the maximum number of polymorphic loci, was detected in the A03 linkage group. No polymorphic alleles were detected on chromosome 10. The polymorphism information content for the 22 polymorphic microsatellite loci varied from 0.52 to 0.98, with an average of 0.89. Genetic diversity analysis revealed that the landraces in the Southern region had more genetic variability than those from the other two regions, and no significant difference was detected between landraces in the Yangtze and the Yellow River Valley regions. These findings are consistent with the history of sinense introduction, with the Southern region being the presumed center of origin for Chinese Asiatic cotton, and with subsequent northeastward extension to the Yangtze and Yellow River Valleys. Cluster analysis, based on simple sequence repeat data for 60 microsatellite loci, clearly differentiated Vietnamese and G. herbaceum landraces from the sinense landrace. No relationship between inter‐variety similarity and geographical ecological region was observed. The present findings indicate that the Southern region landraces may have been directly introduced into the provinces in the middle and lower Yangtze River Valley, where Asiatic cotton was most extensively grown, and further race sinense crops were subsequently produced.(Managing editor: Ya‐Qin Han)

DIVERSITY IN COMMON BEAN LANDRACES (Phaseolus vulgaris L.) FROM BULGARIA AND PORTUGAL

The genetic diversity of landraces is thought to be the economic valuable part of global biodiversity and is considered of paramount importance for future world production. The investigation was performed on 30 common bean landraces (Ph. vulgaris L.) from different geographic origin of Portugal and Bulgaria. The morphological characterization was done according to the IPGRI descriptors (Rome, Italy). Twenty morphological traits were studied in Portuguese and Bulgarian landraces of common bean (Phaseolus vulgaris L.). Accessions number 99E059(BG), 99E0123(BG), PH2(PT) and PH23(PT) are of special interest for breeding purposes.

Allelic Diversification at the C (OsC1) Locus of Wild and Cultivated Rice

Divergent phenotypes are often detected in domesticated plants despite the existence of invariant phenotypes in their wild forms. One such example in rice is the occurrence of varying degrees of apiculus coloration due to anthocyanin pigmentation, which was previously reported to be caused by a series of alleles at the C locus. The present study reveals, on the basis of comparison of its maps, that the C gene appears to be the rice homolog (OsC1) of maize C1, which belongs to the group of R2R3-Myb factors. Two different types of deletions causing a frameshift were detected in the third exon, and both of the deleted nucleotides corresponded to the positions of putative base-contacting residues, suggesting that the Indica and Japonica types carry loss-of-function mutations with independent origins. In addition, replacement substitutions were frequently detected in OsC1 of strains carrying the previously defined C alleles. Molecular population analysis revealed that 17 haplotypes were found in 39 wild and cultivated rices, and the haplotypes of most cultivated forms could be classified into one of three distinct groups, with few shared haplotypes among taxa, including Indica and Japonica types. The genealogy of the OsC1 gene suggests that allelic diversification causing phenotypic change might have resulted from mutations in the coding region rather than from recombination between preexisting alleles. The McDonald and Kreitman test revealed that the changes in amino acids might be associated with selective forces acting on the lineage of group A whose haplotypes were carried by most Asian cultivated forms. The results regarding a significant implication for genetic diversity in landraces of rice are also discussed.

Genetic Diversity In The Lima Bean (Phaseolus Lunatus L.) As Revealed By Chloroplast Dna (Cpdna) Variations

Genetic diversity in the Lima bean (P. lunatus L.) was assessed bymeans of two chloroplast DNA probes. Based on data obtained from 152accessions including wild forms and landraces, the two separateMesoamerican and Andean groups were confirmed and a transition poolof genetic diversity was observed in the two botanical formsconsistent with their distribution range. Three primary centres ofgenetic diversity and one secondary diversification spot are proposedfor the wild Lima bean whereas only two domestication sites areunderlined for the landraces. The importance of human intervention inwidening the distribution range and the genetic diversity inlandraces is discussed.