Local genetic diversity of sorghum in a village in northern Cameroon: structure and dynamics of landraces

We present the first study of patterns of genetic diversity of sorghum landraces at the local scale. Understanding landrace diversity aids in deciphering evolutionary forces under domestication, and has applications in the conservation of genetic resources and their use in breeding programs. Duupa farmers in a village in Northern Cameroon distinguished 59 named sorghum taxa, representing 46 landraces. In each field, seeds are sown as a mixture of landraces (mean of 12 landraces per field), giving the potential for extensive gene flow. What level of genetic diversity underlies the great morphological diversity observed among landraces? Given the potential for gene flow, how well defined genetically is each landrace? To answer these questions, we recorded spatial patterns of planting and farmers’ perceptions of landraces, and characterized 21 landraces using SSR markers. Analysis using distance and clustering methods grouped the 21 landraces studied into four clusters. These clusters correspond to functionally and ecologically distinct groups of landraces. Within-landrace genetic variation accounted for 30% of total variation. The average F _is over landraces was 0.68, suggesting high inbreeding within landraces. Differentiation among landraces was substantial and significant (F _st = 0.36). Historical factors, variation in breeding systems, and farmers’ practices all affected patterns of genetic variation. Farmers’ practices are key to the maintenance, despite gene flow, of landraces with different combinations of agronomically and ecologically pertinent traits. They must be taken into account in strategies of conservation and use of genetic resources.     

微卫星标记分析水稻地方品种30年的遗传变异

为揭示水稻(Oryza sativa)地方品种30年的遗传变异状况,文章通过60个SSR标记,对元阳哈尼梯田农户在20世纪70年代种植的6个(简称"过去的品种")和近10年间种植的对应6个(简称"当前的品种")代表性水稻地方品种进行检测。结果表明,共检测到159个等位基因(Na),等位基因数1～4不等,当前的品种较过去的品种减少7个等位基因。平均每个标记检测到的等位基因数(Na)、有效等位基因数(Ne)、基因型多样性(H′)和位点多态信息含量(PIC)4个指标均为过去的品种高于当前的品种,分别是(Na)为2.567>2.450,(Ne)为2.052>1.968,(H′)为0.768>0.722,(PIC)为0.469>0.439。基于60个SSR标记,过去6个品种间的遗传相似性系数(GS)平均值为0.437,变幅为0.117～0.667,而当前6个品种间平均值为0.473,变幅为0.200～0.700。总的说来,水稻地方品种经过30年自然和人工选择,遗传多样性降低,不同品种存在等位基因大小的差异程度不同。     

我国西南地区玉米地方品种遗传多样性的SSR分子标记分析

利用微卫星(SSR)标记技术和DNA混合取样方法,选取均匀覆盖玉米染色体组的42对SSR引物,检测了来自我国西南地区54个玉米地方品种的遗传多样性。在54个玉米地方品种中检测到256个等位基因,每个SSR标记的等位基因数为2～9个,平均6.1个,说明我国西南地区玉米地方品种遗传多样性丰富。根据遗传相似系数矩阵做出的树状图,将54个玉米地方品种大致划分成4类,来源于同一地区的多数玉米地方品种划分在同一类中,表明西南地区玉米地方品种的地理分布与其遗传背景存在内在联系。从54个玉米地方品种中选出11个,每个品种选取15个单株,共165个DNA单株样品,分析玉米地方品种的遗传结构及其品种内的遗传多样性。对于检测玉米地方品种的遗传多样性,DNA单株样品分析优于DNA混合样品分析,42对相同的SSR引物在11个玉米地方品种中检测到330个等位基因,平均等位基因数A=7.86,有效等位基因数Ae=3.90,平均期望杂合度He=0.69,实际观察杂合度H0=0.37。据遗传结构分析结果,固定指数(F)为0.25～0.79,表明玉米地方品种是典型的混合繁育系统;由于杂合体不足,玉米地方品种群体间及群体内的遗传结构均偏离了Hardy-Weinberg平衡;杂合性基因多样度比率(Fst)平均为0.07,表明品种间和品种内的遗传变异分别占总遗传变异的7%和93%。玉米地方品种内遗传多样性及品种间遗传距离分析结果表明,在我国西南地区,分布在四川的玉米地方品种具有最丰富的遗传变异。经综合分析推测,我国西南地区玉米地方品种最早引进到四川种植,由此向毗邻地区传播扩散。     

Genotyping of DNA pools identifies untapped landraces and genomic regions to develop next-generation varieties

Landraces, that is, traditional varieties, have a large diversity that is underexploited in modern breeding. A novel DNA pooling strategy was implemented to identify promising landraces and genomic regions to enlarge the genetic diversity of modern varieties. As proof of concept, DNA pools from 156 American and European maize landraces representing 2340 individuals were genotyped with an SNP array to assess their genome-wide diversity. They were compared to elite cultivars produced across the 20th century, represented by 327 inbred lines. Detection of selective footprints between landraces of different geographic origin identified genes involved in environmental adaptation (flowering times, growth) and tolerance to abiotic and biotic stress (drought, cold, salinity). Promising landraces were identified by developing two novel indicators that estimate their contribution to the genome of inbred lines: (i) a modified Roger's distance standardized by gene diversity and (ii) the assignation of lines to landraces using supervised analysis. It showed that most landraces do not have closely related lines and that only 10 landraces, including famous landraces as Reid's Yellow Dent, Lancaster Surecrop and Lacaune, cumulated half of the total contribution to inbred lines. Comparison of ancestral lines directly derived from landraces with lines from more advanced breeding cycles showed a decrease in the number of landraces with a large contribution. New inbred lines derived from landraces with limited contributions enriched more the haplotype diversity of reference inbred lines than those with a high contribution. Our approach opens an avenue for the identification of promising landraces for pre-breeding.     

Assessment of ISSR based molecular genetic diversity of Hassawi rice in Saudi Arabia

Inter simple sequence repeat (ISSR) analysis, using 14 primers was performed to estimate genetic diversity among 27 landraces of Hassawi rice growing in Al-Ahsa region of Saudi Arabia and deposited at King Abdulaziz City for Science and Technology with KACST IDs. The average polymorphism produced by 11 selected primers was more than 75%. The analysis of ISSR polymorphism divided the examined rice landraces into two groups; In one group (A), one accession (KACST 191) was clearly delimited as a distant landrace from other 12 landraces grouped in two clusters; cluster I of seven landraces of close geographic distributions; four of them grow at close geographic locations (KACST IDs 32, 183, 184, 185, 186, 187 and 188) and cluster II is comprised of five landraces KACST IDs (190, 308, 352, 353 and 355). In group B, the landraces were more closely related to each other as compared to the landraces of group A. In this group a small cluster of two landraces (KACST 305 & KACST 333) was clearly distant from a large group of three clusters comprised of landraces having KACST IDs 189 & 192, landraces 302, 306, 307, 308 & 310 and landraces with KACST IDs 334, 351, 354, 356 & 357 respectively. These results indicate that ISSR fingerprints are efficient in the identification and resolution of genetic diversity between the landraces of the Hassawi rice and will be an efficient method in the authentication of the rice germplasm in the gene bank of Saudi Arabia.     

Genetic diversity in cultivars and landraces of Oryza sativa subsp. indica as revealed by AFLP markers.

Genetic diversity among 49 Indian accessions of rice (Oryza sativa subsp. indica), including 29 landraces from Jeypore, 12 modern cultivars, and 8 traditional cultivars from Tamil Nadu, was investigated using AFLP markers. In total, nine primer combinations revealed 664 AFLPs, 408 of which were found to be polymorphic. The percentage of polymorphic AFLPs was approximately the same within the cultivars and landraces. Similar results were obtained when genetic diversity values were estimated using the Shannon-Weiner index of diversity. Genetic diversity was slightly higher in the modern cultivars than in the traditional cultivars from Tamil Nadu. Among the landraces from Jeypore, the lowland landraces showed the highest diversity. The present study showed that the process of breeding modern cultivars did not appear to cause significant genetic erosion in rice. Cluster analysis and the first component of principle component analysis (PCA) both showed a clear demarcation between the cultivars and landraces as separate groups, although the genetic distance between them was narrow. The modern cultivars were positioned between the landraces from Jeypore and the traditional cultivars from Tamil Nadu. The second component of PCA further separated medium and upland landraces from lowland landraces, with the lowland landraces found closest to the traditional and modern cultivars.     

中国小麦地方品种内和品种间醇溶蛋白遗传多样性分析

为了揭示中国小麦地方品种内遗传异质性和品种间的遗传多样性,采用A-PAGE方法,对72份来自不同生态区的地方品种进行醇溶蛋白构成分析。结果发现,全部供试地方品种共观察到101条迁移率不同的务带,构成229种醇溶蛋白构型,每个品种醇溶蛋白条带数目为14—24。63份（87．5％）地方品种在品种内具有2种以上醇溶蛋白变异类型,其中,变异类型最多的品种二红皮小麦（ZM004659）30个子粒中有14种之多,多数品种具有2—3种变异类型。品种内醇溶蛋白构型一致的品种共有9个,占12．5％。这表明供试的大多数小麦地方品种内个体间在醇溶蛋白构成上具有遗传异质性。聚类分析表明,相同生态区的地方品种没有整齐地聚为一类。     

凉山州马铃薯栽培品种的遗传多样性分析

利用SSR分子标记技术对凉山州马铃薯地方品种、自育品种和各地育成品种共计60份进行了遗传多样性分析,筛选出16对有效SSR引物。采用筛选的16对引物在供试材料中共检测到68个位点,其中多态性位点42个占总扩增位点的61.76%,平均PIC值为0.4717。通过NTSYSpc 2.0对所有材料间的遗传距离进行计算,平均遗传距离在2.43~3.96之间。使用MEGA4分析软件将供试材料分成3大类,2个凉山州地方品种在聚类图中最先被分离出来。利用PoPGEN将凉山州地方种和其余材料分成两类,。上述结果表明凉山州地方种与试验中其他品种的遗传基础差异较大,是较好的资源材料。该研究为凉山州地方马铃薯品种在今后育种中的应用提供了部分参考依据。     

山东保存小麦种质资源面粉白度分析

对2068份小麦种质资源进行了面粉白度测定和高白度小麦种质子粒硬度测定。结果表明,山东小麦地方品种、山东小麦育成品种和省外引进小麦品种面粉白度值的分布范围分别为63.9～82.9、63.1～83.8和67.2～84.2。筛选出面粉白度值大于80的小麦种质342份(包括白度值大于83的种质26份),其中地方品种22份,山东育成品种(系)228份,省外引进种质92份。从高白度小麦种质资源中,筛选出子粒硬度指数≥50符合高白度强筋、中强筋或中筋的种质资源18份,对培育中筋以上高白度小麦新品种,以满足人们口味和健康保障具有重要意义。     

Antixenosis,tolerance and genetic analysis of some rice landraces for resistance to Nilaparvata lugens (Stål.)

Twenty-six rice landraces from West Bengal, India were evaluated for antixenosis and tolerance against brown planthopper (BPH) biotype 4 at the Bidhan Chandra Krishi Viswavidyalaya (BCKV), West Bengal. High levels of resistance were observed in six landraces, namely Badshabhog, Gamra, Haldichuri, Janglijata, Kalabhat and Khara. These phenotypically resistant rice landraces including Ptb33 exhibited lowest feeding rate, fecundity, nymphal and adult preference, survival, plant dry weight loss per mg of BPH dry weight produced (PDWL), and higher functional plant loss index (FPLI), more days to wilt and unhatched eggs compared with the susceptible check Swarna. All the landraces were classified into four major clusters at 10 unit distance by the scale of similarity during genetic diversity analysis through 21 gene-linked SSR markers of BPH resistance. Some phenotypically resistant landraces were gathered under the major cluster I indicating their analogous genetic history, while some were grouped with susceptible landraces exhibiting their genetic variation. The resistant landraces can be used as potential donors in the breeding programme for the development of rice varieties with resistance to BPH.     

Genetic diversity amongst landraces of rye (Secale cereale L.) from northern Europe

Genetic variation and diversity were estimated for three improved varieties and 18 landraces of Secale cereale, originating from the northern Europe. This material was compared with eight improved varieties and 16 landraces from Sweden, which were analysed before. The analysis used starch gel electrophoresis with the enzymes ACO, GPI, MDH, PGD and PGM and resulted in one fixed locus and seven polymorphic loci. Most of the genetic diversity was found within the accessions and it was very small between accessions. The results show that the landraces from Germany and Norway have a low genetic variation compared to the other landraces in this study. This can possibly be explained with a small original sample size of some accessions. However, in the dendrogram these accessions are well separated. The landraces from Sweden and Finland showed a high genetic variation, which is almost the same for all these accessions. In the dendrogram all of the Finnish landraces and 11 of the Swedish ones were grouped together with a very small diversity index; they can almost be considered as part of the same accession. This is probably due to the fact that a high number of Finnish immigrants arrived in Sweden during the 17th century bringing their own rye material. The early Finnish rye landraces may have the same original source. The data also show that landraces as well as improved varieties have a high heterozygosity but they are separated in the dendrogram into different clusters. The currently used varieties show a large genetic distance variation, different from that in the landraces.     

Is there an optimum level of diversity in utilization of genetic resources?

Key message

Capitalizing upon the genomic characteristics of long-term random mating populations, sampling from pre-selected landraces is a promising approach for broadening the genetic base of elite germplasm for quantitative traits.

Abstract

Genome-enabled strategies for harnessing untapped allelic variation of landraces are currently evolving. The success of such approaches depends on the choice of source material. Thus, the analysis of different strategies for sampling allelic variation from landraces and their impact on population diversity and linkage disequilibrium (LD) is required to ensure the efficient utilization of diversity. We investigated the impact of different sampling strategies on diversity parameters and LD based on high-density genotypic data of 35 European maize landraces each represented by more than 20 individuals. On average, five landraces already captured ~95% of the molecular diversity of the entire dataset. Within landraces, absence of pronounced population structure, consistency of linkage phases and moderate to low LD levels were found. When combining data of up to 10 landraces, LD decay distances decreased to a few kilobases. Genotyping 24 individuals per landrace with 5k SNPs was sufficient for obtaining representative estimates of diversity and LD levels to allow an informed pre-selection of landraces. Integrating results from European with Central and South American landraces revealed that European landraces represent a unique and diverse spectrum of allelic variation. Sampling strategies for harnessing allelic variation from landraces depend on the study objectives. If the focus lies on the improvement of elite germplasm for quantitative traits, we recommend sampling from pre-selected landraces, as it yields a wide range of diversity, allows optimal marker imputation, control for population structure and avoids the confounding effects of strong adaptive alleles.

     

Introgression from modern hybrid varieties into landrace populations of maize (Zea mays ssp. mays L.) in central Italy

Landraces are domesticated local plant varieties that did not experience a deliberate and intensive selection during a formal breeding programme. In Europe, maize landraces are still cultivated, particularly in marginal areas where traditional farming is often practiced. Here, we have studied the evolution of flint maize landraces from central Italy over 50 years of on-farm cultivation, when dent hybrid varieties were introduced and their use was widespread. We have compared an 'old' collection, obtained during the 1950s, before the introduction of hybrids, and a recent collection of maize landraces. For comparison, a sample of maize landraces from north Italy, and of improved germplasm, including hybrids and inbred lines were also used. A total of 296 genotypes were analysed using 21 microsatellites. Our results show that the maize landraces collected in the last 5–10 years have evolved directly from the flint landrace gene pool cultivated in central Italy before the introduction of modern hybrids. The population structure, diversity and linkage disequilibrium analyses indicate a significant amount of introgression from hybrid varieties into the recent landrace populations. No evidence of genetic erosion of the maize landraces was seen, suggesting that in situ conservation of landraces is an efficient strategy for preserving genetic diversity. Finally, the level of introgression detected was very variable among recent landraces, with most of them showing a low level of introgression; this suggests that coexistence between different types of agriculture is possible, with the adoption of correct practices that are aimed at avoiding introgression from undesired genetic sources.     

中国粳稻地方品种孕穗期耐冷性评价及聚类分析

用原产于中国18个省的329份粳稻地方品种为材料,分析了自然低温和冷水胁迫下不同省份粳稻地方品种孕穗期耐冷性及主要农艺性状表型差异和聚类特点。结果表明,在自然低温和冷水胁迫下各省份粳稻地方品种的孕穗期耐冷性状及主要农艺性状有明显的差异。在自然低温和冷水胁迫下,天津、四川和台湾品种的结实率及冷水反应指数均较高,表现较强的孕穗期耐冷性和迟钝的冷水反应。云南品种在自然低温下表现为较强的孕穗期耐冷性（结实率）,而在冷水胁迫下播种至抽穗天数和株高的冷水反应指数较高,表现为迟钝的冷水反应。从总体趋势上看,自然低温和冷水胁迫下,除个别省份外,纬度相对较高的北方省份品种的孕穗期耐冷性（结实率）强于纬度相对较低的南方省份品种。此外,在自然低温和冷水胁迫下,各省粳稻地方品种的聚类结果总体上与各省品种的地理位置及其耐冷性有密切的联系,而在冷水胁迫下品种的聚类结果与品种地理位置的关系比自然低温下更为密切。     

Unlocking the Genetic Diversity of Maize Landraces with Doubled Haploids Opens New Avenues for Breeding

Landraces are valuable genetic resources for broadening the genetic base of elite germplasm in maize. Extensive exploitation of landraces has been hampered by their genetic heterogeneity and heavy genetic load. These limitations may be overcome by the in-vivo doubled haploid (DH) technique. A set of 132 DH lines derived from three European landraces and 106 elite flint (EF) lines were genotyped for 56,110 single nucleotide polymorphism (SNP) markers and evaluated in field trials at five locations in Germany in 2010 for several agronomic traits. In addition, the landraces were compared with synthetic populations produced by intermating DH lines derived from the respective landrace. Our objectives were to (1) evaluate the phenotypic and molecular diversity captured within DH lines derived from European landraces, (2) assess the breeding potential (usefulness) of DH lines derived from landraces to broaden the genetic base of the EF germplasm, and (3) compare the performance of each landrace with the synthetic population produced from the respective DH lines. Large genotypic variances among DH lines derived from landraces allowed the identification of DH lines with grain yields comparable to those of EF lines. Selected DH lines may thus be introgressed into elite germplasm without impairing its yield level. Large genetic distances of the DH lines to the EF lines demonstrated the potential of DH lines derived from landraces to broaden the genetic base of the EF germplasm. The comparison of landraces with their respective synthetic population showed no yield improvement and no reduction of phenotypic diversity. Owing to the low population structure and rapid decrease of linkage disequilibrium within populations of DH lines derived from landraces, these would be an ideal tool for association mapping. Altogether, the DH technology opens new opportunities for characterizing and utilizing the genetic diversity present in gene bank accessions of maize.     

Convergent adaptations: bitter manioc cultivation systems in fertile anthropogenic dark earths and floodplain soils in central amazonia

SHIFTING CULTIVATION IN THE HUMID TROPICS IS INCREDIBLY DIVERSE, YET RESEARCH TENDS TO FOCUS ON ONE TYPE: long-fallow shifting cultivation. While it is a typical adaptation to the highly-weathered nutrient-poor soils of the Amazonian terra firme, fertile environments in the region offer opportunities for agricultural intensification. We hypothesized that Amazonian people have developed divergent bitter manioc cultivation systems as adaptations to the properties of different soils. We compared bitter manioc cultivation in two nutrient-rich and two nutrient-poor soils, along the middle Madeira River in Central Amazonia. We interviewed 249 farmers in 6 localities, sampled their manioc fields, and carried out genetic analysis of bitter manioc landraces. While cultivation in the two richer soils at different localities was characterized by fast-maturing, low-starch manioc landraces, with shorter cropping periods and shorter fallows, the predominant manioc landraces in these soils were generally not genetically similar. Rather, predominant landraces in each of these two fertile soils have emerged from separate selective trajectories which produced landraces that converged for fast-maturing low-starch traits adapted to intensified swidden systems in fertile soils. This contrasts with the more extensive cultivation systems found in the two poorer soils at different localities, characterized by the prevalence of slow-maturing high-starch landraces, longer cropping periods and longer fallows, typical of previous studies. Farmers plant different assemblages of bitter manioc landraces in different soils and the most popular landraces were shown to exhibit significantly different yields when planted in different soils. Farmers have selected different sets of landraces with different perceived agronomic characteristics, along with different fallow lengths, as adaptations to the specific properties of each agroecological micro-environment. These findings open up new avenues for research and debate concerning the origins, evolution, history and contemporary cultivation of bitter manioc in Amazonia and beyond.     

龙生型花生的遗传多样性

龙生型花生(Arachis hypogaea var.hirsute)是中国引进最早、种植最早的花生类型。经过不断地自然选择和人工选择,形成了许多各具特色的地方品种,并逐渐形成了次生中心。本实验对15份龙生型花生资源在植物学性状和品质性状及分子水平上进行了系统研究。结果表明:龙生型花生在植物学性状和品质性状上具有丰富的遗传多样性,在分子水平上差异也较大。变异系数在5.10~34.60之间,多样性指数在1.17~2.04之间,同时两者的变化趋势相反。基于植物学性状和品质性状上的聚类分析在阀值为6.5将龙生型花生分为两大类,一类主要包括广西的品种,另一类包括其它省份的品种;基于AFLP分析的聚类结果在阀值为0.39处分为5类,一类主要包括广西的品种,其它4类包括其它省份的品种。     

龙生型花生的遗传多样性

龙生型花生(Arachis hypogaea var.hirsute)是中国引进最早、种植最早的花生类型。经过不断地自然选择和人工选择,形成了许多各具特色的地方品种,并逐渐形成了次生中心。本实验对15份龙生型花生资源在植物学性状和品质性状及分子水平上进行了系统研究。结果表明:龙生型花生在植物学性状和品质性状上具有丰富的遗传多样性,在分子水平上差异也较大。变异系数在5.10-34.60之间,多样性指数在1.17-2.04之间,同时两者的变化趋势相反。基于植物学性状和品质性状上的聚类分析在阀值为6.5将龙生型花生分为两大类,一类主要包括广西的品种,另一类包括其它省份的品种;基于AFLP分析的聚类结果在阀值为0.39处分为5类,一类主要包括广西的品种,其它4类包括其它省份的品种。     

Role of seed flow on the pattern and dynamics of pearl millet (<Emphasis Type="Italic">Pennisetum glaucum</Emphasis> [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.     

中国地方黄牛的Y染色体遗传多样性及其进化起源

中国黄牛的进化起源与遗传多样性一直是国内外动物遗传学家感兴趣的课题之一.本文主要从Y染色体的形态多样性和Y染色体特异性微卫星标记遗传多态性两个方面对中国地方黄牛的遗传多样性和进化起源进行了综述.中国地方黄牛Y染色体具有中着丝粒、亚中着丝粒和近端着丝粒3种类型,这说明中国地方黄牛起源于普通牛和瘤牛.利用Y染色体特异性微卫星标记对中国地方黄牛Y染色体单倍型分布特征及Y染色体基因流模式的分析表明,北方种群中普通牛单倍型频率最高,瘤牛单倍型在南方种群中占优势;在中国不同地域,瘤牛Y染色体单倍型频率呈现自南而北、自东而西逐渐降低的趋势,这再次证实了中国黄牛主要来源于普通牛和瘤牛,这可能是这两类牛群在长期的历史进化过程中,分别从东南方向和西北方向进入我国,并在中原地区汇合的结果.本文为中国地方黄牛品种资源保护和杂交育种工作提供了参考依据.