基于形态学性状和SSR标记的花生品种遗传多样性分析和特异性鉴定

以101份南方花生区试品种为材料,利用形态学性状和SSR标记进行品种遗传多样性分析和特异性鉴定。结果表明, 29个形态学性状中有7个无多样性,其余22个的多样性指数为0.23～0.77,平均为0.43。在相似系数为0.76处,将供试品种划分为七大类群,同一育种单位的品种倾向于聚在一起。用40个SSR标记共检测出167个等位基因,单个标记检测的等位基因数2～6个,平均为4.18个。标记的多态性信息量(PIC)差异较大,最大为0.79,最小为0.26,平均为0.55。在相似系数为0.70处,供试品种可被划分为六大类群,同一省份育成的品种多聚为一类。Mantel检验发现品种间的形态学性状和SSR标记的相似系数矩阵相关性弱(r=0.36),SSR标记无法取代形态学性状单独用于花生品种特异性鉴定,但两者相结合能有效提高花生品种特异性鉴定的准确性。     

Discovery and characterization of a molecular marker for <Emphasis Type="Italic">Sclerotinia minor</Emphasis> (Jagger) resistance in peanut

The production of cultivated peanut, an important agronomic crop throughout the United States and the world, is consistently threatened by various diseases and pests. Sclerotinia minor Jagger (S. minor), the causal agent of Sclerotinia blight, is a major threat to peanut production in the Southwestern US, Virginia and North Carolina. Although information on the variability of morphological traits associated with Sclerotinia blight resistance is plentiful, no molecular markers associated with resistance have been reported. The identification of markers would greatly assist peanut geneticists in selecting genotypes to be used in breeding programs. The main objective of this work was to use simple sequence repeat (SSR) primers previously reported for peanut to identify a molecular marker associated with resistance to S. minor. Out of 16 primer pairs used to examine peanut genomic DNA from 39 different genotypes, one pair produced bands at approximately 145 and 100 bp, consistent with either S. minor resistance or susceptibility, respectively. Cloning and sequencing of these bands revealed the region is well conserved among all genotypes tested with the exception of the length of the SSR region, which varies with disease resistance levels. This is the first report of a molecular marker associated with resistance to Sclerotinia blight in peanut. The identification of this marker and development of a PCR-based screening method will prove to be extremely useful to peanut breeders in screening germplasm collections and segregating populations as well as in pyramiding S. minor resistance with other desirable traits into superior peanut lines.     

Assessment of wheat variety stability using SSR markers

In International Union for the Protection of New Varieties of Plants member countries, assessment of wheat variety stability is a statutory requirement before new varieties are registered and plant breeders’ rights are granted. However, it is impossible to test the stability of varieties accurately and quickly, or to assess the stability of a large number of varieties in a short time based on the morphological traits defined by the national standard. The objective of this study was to establish method and procedure of wheat variety stability assessment using SSR markers as a replacement for morphological observations. In preliminary study, the methods to identify non-homozygous SSR loci and calculate the homozygous SSR loci ratio (SSR–HLR) of wheat varieties were established. On this basis, the genotypes at 347 molecular markers loci of 20 advanced lines demonstrated that SSR–HLRs were 84.7–94.8 % in the F₄ lines, 96.1–99.4 % in the F₅ lines, and ≥98 % in the F₆ lines, respectively. Eighty of 347 markers with good polymorphism, stable PCR amplification, and high resolving power of genotyping were recommended to detect SSR–HLR for 633 wheat regional trial varieties. Comparing morphological observation, the varieties with SSR–HLR >95 % were deemed stable; the varieties with SSR–HLR <91 % were deemed unstable; the varieties with SSR–HLR ranging from 91 to 95 % were required field identification for stability assessment. Based on the relationship between the homozygous SSR loci ratio and wheat variety stability, procedures for the assessment of wheat variety stability using SSR markers were established.     

Phenotypic diversity in cold-tolerant peanut (<Emphasis Type="Italic">Arachis hypogaea</Emphasis> L.) germplasm

Tolerance to low temperature is an important prerequisite for optimal performance of peanut (Arachis hypogaea L.) in a number of temperate peanut-growing environments. One hundred fifty-eight peanut accessions belonging to five botanical types, known to be tolerant to low temperature (12°C) at germination, were evaluated for phenotypic diversity for 15 morphological traits in the 2001 rainy season and for 15 agronomic and two seed quality traits in the 2001 rainy and 2001/2002 post-rainy seasons. Analysis of data, using the residual maximum-likelihood approach indicated that variance components due to genotypes were significant for all traits in the rainy and for all but two traits in the post-rainy season. Clustering based on scores of nine principle components delineated four clusters. The cold-tolerant genotypes and the standard control cultivars in the four clusters differed in mean, variance, and range both during rainy and post-rainy seasons for a range of agronomic traits, indicating the diversity among the clusters. The cold-tolerant accessions were superior to control cultivars for several agronomic traits compared with their respective controls in both the rainy and post-rainy seasons, so their use in breeding should result in genetically diverse cold-tolerant high-yielding peanut cultivars.     

河南省审定花生品种的指纹图谱构建

利用14个SSR标记构建了河南省2015年之前选育并审定的90个花生品种的DNA指纹图谱,用14个SSR标记产生的95个多态性位点可将90个花生品种完全区分开,其中84个品种间有≥2个位点的差异,在剩余的3对品种中,每对仅有1个差异位点。聚类分析结果表明,在遗传相似系数0.98处,90个花生品种被聚集成88类,有2对品种分别聚集在一起,是由于它们每一个品种分别以另一个品种作亲本选育而成,仅有1个差异SSR位点,表明所构建的指纹图谱是有效的。以遗传相似系数0.95为划分标准,有74.4%的品种具有特异性,与其他作物相比,河南省育成花生品种总体上亲缘关系相对较近。根据60个SSR标记的群体结构分析,90个花生品种可以分为3个亚群,与根据分枝开花习性和荚果类型的分类相吻合,亚群划分情况与聚类分析结果基本一致。     

Simple sequence repeats for genetic analysis in pear

The development of highly informative DNA markers, such as simple sequence repeats (SSRs), is essential for breeding to select agronomically important traits and for genetic studies in pear. We developed SSR markers by using two approaches, RAHM (random amplified hybridization microsatellites) and 5' anchored PCR methods. Segregation analysis of the SSRs revealed that amplified fragments were derived from the same loci, using 3 sets of progenies from crosses between pear varieties. Genetic diversity was characterized using 32 varieties, including 10 from Japanese pear (Pyrus pyrifolia), 9 from Chinese pear (P. bretschneideri, P. ussuriensis), 10 from European pear (P. communis) as well as 3 wild relatives (P. calleryana). Diversity of SSR genotypes was observed among species as well as within species and 65 putative alleles were detected. The use of seven SSR markers was sufficient to differentiate between all of the 32 varieties. This revised version was published online in August 2006 with corrections to the Cover Date.     

Genetic Variation for Regenerative Response in Immature Leaflet Cultures of the Cultivated Peanut,Arachis hypogaea*

Forty-seven genotypes of the cultivated peanut, Arachis hypogaea L., were screened for regenerative responses of immature leaflet cultures on two media varying in the auxin: cytokinin ratio. Statistical analysis revealed significant media and genotype differences for rhizogenesis plus media differences for callus proliferation but no differences for shoot formation. When genotypes were categorized according to botanical types, differences between subspecies were observed for rhizogenesis. Cultivars of the Virginia botanical type (subspecies hypogaea) were significantly different from either the Valencia or Spanish botanical types (both subspecies fastigiata). Overall, rhizogenesis varied from 0 to 70% among all genotypes. Shoot production was low (30%) while callus proliferation was extremely high (70%).     

Genetic diversity,structure and fruit trait associations in Greek sweet cherry cultivars using microsatellite based (SSR/ISSR) and morpho-physiological markers

It is important to couple phenotypic analysis with genetic diversity for germplasm conservation in gene bank collections. The use of molecular markers supports the study of genetic marker-trait associations of biological and agronomic interest on diverse genetic material. In this report, 19 Greek traditional sweet cherry cultivars and two international cultivars, which were used as controls, were grown in Greece and characterized for 17 morpho-physiological traits, 15 simple sequence repeat (SSR) loci and 10 inter simple sequence repeat (ISSR) markers. To our knowledge, this is the first report on molecular genetic diversity studies in sweet cherry in Greece. Principal component analysis (PCA) of nine qualitative and eight quantitative morphological parameters explain over 77.33% of total variability in the first five axes. The SSR markers yielded a combined matching probability ratio (MPR) of 9.569 × e−12. The 15 SSR loci produced a total of 92 alleles. Ten ISSR primers generated 91 bands, with an average of 9.1 bands per primer. Expected heterozygosity (gene diversity) values of 15 SSR loci and 10 ISSR markers averaged at 0.683 and 0.369, respectively. Based on stepwise multiple regression analysis (MRA), SSR alleles were found associated with harvest time and fruit polar diameter. Furthermore, three ISSR markers were correlated with fruit harvest and soluble solids and four ISSR markers were correlated with fruit skin color. Stepwise MRA identified six SSR alleles associated with harvest time with a high correlation (P < 0.001), with linear associations with high F values. Hence, data analyzed by the use of MRA could be useful in marker-assisted breeding programs when no other genetic information is available.     

中国花生核心种质的建立及与ICRISAT花生微核心种质的比较

以中国花生种质资源数据库中记录的6 390份花生资源为材料, 以其基本数据、特征数据和评价数据为信息, 采用分层分组聚类以及随机取样与必选资源相结合的方法, 构建了由576份资源组成的花生核心种质, 占基础收集品的9.01%。除出仁率外, 核心种质与基础收集品种间的其他14个性状平均值和多样性指数差异均不明显, 表明本研究建立的核心种质是有效的。与ICRISAT花生微核心种质的比较, 中国花生资源在龙生型和珍珠豆型方面具有优势, 叶片长、叶片宽、种子长、种子宽的遗传多样性丰富; 而ICRISAT花生资源在多粒型和普通型方面具有优势, 且植株高度和总分枝数的遗传多样性比中国花生资源丰富。     

抗青枯病花生种质的遗传多样性

以栽培种花生2个亚种4个植物学类型的31份对青枯病具有不同抗性的种质为材料,通过SSR和AFLP技术分析了其DNA多样性,并与通过形态和种子品质性状揭示的表型多样性进行了比较。结果表明,不同类型的抗青枯病花生品种之间存在丰富的DNA多样性,SSR揭示的品种间遗传距离大于AFLP揭示的品种间遗传距离,基于二者的聚类分析结果趋势一致,结合花生的植物学类型、地理来源和系谱分析,以SSR的聚类结果与表型性状的聚类结果更为吻合。感病优质高产品种“中花5号”与密枝亚种的普通型和龙生型的抗病材料的差异很大,与育种中被广泛利用的抗源“协抗青”和“台山三粒肉”的差异相对较小,与“远杂9102”的差异更小。     

Genetic Dissection of Allelic Loci Associated with Economic Traits of Upland Cottons in Xinjiang

[Objective] We completed anassociation analysis of economic traits for upland cotton using simple sequence repeat (SSR) markers. We then explored the allelic variation sites to analyze the genetic basis of economically important traits, studied the genetic mechanism of Xinjiang upland cotton, and aimed to accelerate efficient breeding of upland cotton. [Method] We carried out polymorphic scanning on 156 upland cotton varieties in Xinjiang by screening 73 pairs of SSR markers encompassing the whole cotton genome. We constructed boxplot maps using R statistical computing software and graphics language and used TASSEL software to correlate yield or fiber quality traits with significant allelic variation loci. [Results] We obtained 10 allelic variation loci related to yield traits using the correlation analysis of Xinjiang upland cotton varieties from six different environments. The interpretation rate of phenotypic variation ranged from 6.69% to 9.88% with an average of 8.43%. Twenty-three allelic variation loci associated with fiber quality traits and phenotypic variation interpretation rates ranged from 3.73% to 13.22% with an average of 7.52%. The 22 detected quantitative trait loci were reported in previous studies and 10 showed the same associated traits as previously reported. [Conclusion] The population genetic structure of Xinjiang upland cotton varieties is simple, the linkage disequilibrium level is low, and the phenotypic traits show a stable trend under six environments. Using association analysis, we discovered unique allelic variation genes related to yield and fiber quality and diverse allele loci.     

ICRISAT花生微核心种质农艺性状和黄曲霉抗性关联分析

以国际半干旱热带地区作物研究所(ICRISAT)花生微核心种质146份资源为品种,鉴定农艺性状和黄曲霉抗性,用26对SSR引物检测多态性位点,在分析连锁不平衡、群体结构和Kinship的基础上进行关联分析。连锁不平衡的分布显示R²平均值为0.185,表明26对SSR引物扩增的120个位点之间具有较低的连锁不平衡程度。群体结构分析结果将146份花生品种分为2个亚群,分别对应疏枝亚种和密枝亚种,与植物学分类和遗传分化分析的结果基本一致。关联分析表明,共有39个位点与10个农艺性状(株高、总分枝数、第一分枝数、小叶宽、结果分枝数、百果重、出仁率、单株生产力、种子长、种子宽)相关联,表型变异解释率为1.50%~20.34%,16个SSR位点与黄曲霉侵染病情指数、黄曲霉产毒量相关联,表型变异解释率为5.23%~17.19%,与农艺性状、黄曲霉抗性同时相关联的SSR位点有13个。关联位点的等位变异效应分析表明,10个农艺性状和2个黄曲霉抗性性状共有63个增效等位变异和47个减效等位变异,并发掘了ICG6022等携有优良等位变异的载体品种。     

An SSR-based molecular genetic map of cassava

Summary Microsatellites or simple sequence repeats (SSR) are the markers of choice for molecular genetic mapping and marker-assisted selection in many crop species. A microsatellite-based linkage map of cassava was drawn using SSR markers and a F₂ population consisting of 268 individuals. The F₂ population was derived from selfing the genotype K150, an early yielding genotype from an F₁ progeny from a cross between two non-inbred elite cassava varieties, TMS 30572 and CM 2177-2 from IITA and CIAT respectively. A set of 472 SSR markers, previously developed from cassava genomic and cDNA libraries, were screened for polymorphism in K150 and its parents TMS 30572 and CM 2177-2. One hundred and twenty two polymorphic SSR markers were identified and utilized for linkage analysis. The map has 100 markers spanning 1236.7 cM, distributed on 22 linkage groups with an average marker distance of 17.92 cM. Marker density across the genome was uniform. This is the first SSR based linkage map of cassava and represents an important step towards quantitative trait loci mapping and genetic analysis of complex traits in M. esculenta species in national research program and other institutes with minimal laboratory facilities. SSR markers reduce the time and cost of mapping quantitative trait loci (QTL) controlling traits of agronomic interest, and are of potential use for marker-assisted selection (MAS).     

Recurrent selection progress in a population derived from an interspecific peanut cross

Summary Two cycles of recurrent selection for yield were previously conducted using a population of Arachis hypogaea L.-like tetraploid hybrid derivatives selected from among the progeny of a cross between A. hypogaea and A. cardenasii Krap. et Greg. nom. nud., a diploid species with resistance to late leafspot (Cercosporidium personatum (Burk. and Curt.) Deighton). Using the 10 highest yielding parents from each of the above cycles of recurrent selection, a study was conducted for 12 morphological traits and susceptibility to leafspot infection in a replicated test at a single location. The two parents used to initiate the interspecific hybrid population (PI 261942-3 and A. cardenasii) as well as two adapted cultivars (Florigiant and NC 7) were included as checks. The objectives of the study were to determine the amount of genetic variation remaining in the population after two cycles of recurrent selection in order to predict whether further progress from selection could be expected and determine the potential for utilizing wild species for the improvement of quantitative traits in peanut. The results indicate that significant levels of genetic variation remain in the population after two cycles of recurrent selection for all traits measured, including several components of yield and leafspot resistance. This suggests that continued progress in population improvement from further cycles of selection should be possible while enhancing the genetic diversity of cultivated peanut germplasm.Paper no. 12347 of the Journal Series of the North Carolina Agric. Res. Serv., Raleigh, NC 27695-7643. This work was partially funded by the Peanut CRSP, USAID grant number DAN-4048-G-SS-2065-00. Recommendations do not represent an official position or policy of USAID.     

Association analysis of fibre traits in Gossypium arboreum accessions

Advances in the use of diploid Asiatic species in cotton breeding require an understanding of the relatedness and ancestry of diploid cotton accessions, and identification of simple sequence repeat (SSR) markers associated with agronomically important phenotypic traits, for example, fibre quality. Fifty‐six Gossypium arboreum germplasm accessions introduced from nine regions of Africa, Asia and Europe were evaluated for eight fibre characters (lint percentage, lint colour, elongation, micronaire, strength, 50% span length, 2.5% span length and maturity%) and genotyped with 98 SSR markers. When viewed across all accessions most of the SSR markers were polymorphic. Population structure analysis identified six main clusters for the accessions which corresponded to different geographic regions, indicating agreement between genetic and predefined populations. The general linear model method was used to disclose marker–trait associations. Marker–trait associations were investigated by fitting single marker regression models for phenotypic traits on marker band intensities with correction for population structure. This paper illustrates the potential of association mapping in diploid cotton, because existing phenotypic data, a modest number of SSR markers, and a pioneering statistical analysis, identified interesting associations.     

Morphological, cytological and disease resistance studies of the intersectional hybrid between Arachis hypogaea L. and A. glabrata Benth.

Arachis glabrata Benth, variety glabrata collector GK 10596 (PI276233; ICG 8176) belonging to section Rhizomatosae has resistance to rust, late leaf spot and viral diseases. A. hypogaea L. cv MK 374 (section Arachis) is susceptible to rust, late leaf spot and to the viral diseases peanut stripe, peanut mottle and peanut bud necrosis. Hybrids between A. hypogaea cv MK 374 and A. glabrata were produced after inter specific pollinations and embryo culture. The hybrids produced had morphological characters of both parents plus floral abnormalities not seen in either parent. It was possible to identify the hybrids by esterase isozyme analysis when still in culture. Cytological research showed variable chromosome association and also homeology between the genomes of A. hypogaea and A. glabrata. The hybrids inherited resistance to rust, late leaf spot, peanut bud necrosis and peanut stripe diseases from the pollen parent A. glabrata. This revised version was published online in August 2006 with corrections to the Cover Date.     

Construction of a genetic map of melon with molecular markers and horticultural traits, and localization of genes associated with ZYMV resistance

Abstract: A partial linkage map of melon was constructed from a cross between PI414723 and Dulce. Twenty-two SSR, 46RAPD, 2 ISSR markers and four horticultural markers [female flower form (a), Fusarium resistance, striped epicarp (st), and fruit flesh pH (pH)] were analyzed in an F₂/F₃ population to produce a map spanning 14 linkage groups. We report for the first time map positions for the st, a, and pH genes. One SSR marker was tightly linked to pH. Mapping the a gene for the female flower form to molecular linkage group 4 enabled the merging of the map of horticultural traits with the of molecular markers in this region. Using the 22 SSR markers of this map, two of the three postulated ZYMV resistance genes were located using a BC₁ population (PI414723 recurrent parent). One SSR marker was tightly linked to a ZYMV resistance gene, designated Zym-1. This revised version was published online in August 2006 with corrections to the Cover Date.     

Identification of a major QTL for adult plant resistance to coffee leaf rust (Hemileia vastatrix) in the natural Timor hybrid (Coffea arabica x C. canephora)

Most of the commercial varieties of coffee (Coffea arabica L.) derived from the Timor hybrid (TH) have been shown to contain major genes for coffee leaf rust (CLR) resistance. To identify markers tightly linked to such genes, an F₂ mapping population derived from a cross between ‘Caturra’ (susceptible variety) and the TH‐derived DI.200 line (highly resistant) was generated. Using expressed sequence information and a bioinformatics approach, both targeted region amplified polymorphism (TRAPs) markers and simple sequence repeat (SSR) markers were identified. Phenotypic evaluations in the field and under controlled conditions confirmed the existence of one quantitative trait locus for CLR resistance. Four candidate SSR markers were associated with high CLR resistance. They spanning a region of 2.5 cM designated Q_{CLR_4} located within chromosome 4 of the international C. canephora map. The presence of this region was confirmed in a set of elite lines and commercial varieties. The Q_{CLR_4} region corresponds to a new and genetically independent S_H locus that could potentially be useful in gene pyramiding with other genes to enhance rust resistance in TH derivatives.     

Comparisons of genetic and morphological distance with heterosis between Medicago sativa subsp. sativa and subsp. falcata

Biomass yield heterosis has been shown to exist between Medicago sativasubsp. sativa and Medica gosativa subsp. falcata. The objective of this study was to gain a better understanding of what morphological and genetic factors were most highly correlated with total biomass yield heterosis. We calculated genetic distances among nine sativa and five falcate genotypes based on amplified fragment length polymorphism (AFLP) and simple sequence repeat (SSR) DNA markers. Genetic distance did not correlate with specific combining ability (SCA) or mid-parent heterosis. In contrast, a morphological distance matrix based on seventeen agronomic and forage quality traits was significantly correlated with heterosis; the agronomic traits of maturity, midseason regrowth, and autumn regrowth showed strong association with heterosis. Heterosis was also correlated with subspecies. We suggest that in many cases progeny heterosis can be accounted for by the interaction of genes controlling morphologically divergent traits between the parents. In other cases, progeny heterosis could also be due to divergence between the parents at particular genetic loci that do not control field-level phenotypic differences. Genetic distanceper se between parental genotypes, based on neutral molecular markers, however, does not reflect the potential of individual genotypes to produce heterosis in their progeny. This revised version was published online in August 2006 with corrections to the Cover Date.