Fungal diversity in pigeonpea (Cajanus cajan (L.) Millspaugh) cropping system of calcareous soil

Soil mycofloral diversity plays a pivotal role in crop production and is an integral part of any ecosystem. Pigeonpea cropping system provides a congenial environment to soil microbes by fixing nitrogen and solubilizing phosphorus which in turn provides sufficient nutrients for their prolific growth. The present study was undertaken to know the fungal diversity in calcareous soil of Bihar region in India, which are not supportive to growth of many fungi owing to high calcium content. Soil samples were collected from pigeonpea cropping system treated with native and commercial isolates of phosphorus solubilizing bacteria (PSB) and plant growth promoting rhizobacteria (PGPR) along with Rhizobium. Thirty-seven species belonging to seven genera and a group of unidentified species were isolated. Aspergillus and Penicillium were the dominant genera in all the treatments. Absidia and Cunnighmella were distributed only once as rare genera. Though single species of Pythium, Rhizopus, Periconia, Geotrichum and Gliocladium genera were recorded but their occurrence was even in all the treatments. The diversity and equitability index were not varied much in different treatments except one. The deuteromucetous fungi occupied the highest space followed by zygomycetous, mycelia sterilia and mastigomycetous fungi.     

Development of simple sequence repeat (SSR) markers and their use in identification of Dendrobium varieties

The aim of this study was to develop simple sequence repeat (SSR) markers for Dendrobium varieties/species, many of which have medicinal and horticultural values. Two genomic DNA libraries of Dendrobium Sonia enriched with GA repeats and CA repeats were constructed. Fourteen polymorphic SSR markers were identified when screened against 42 popular commercial Dendrobium hybrids. The average allele number was 12.0 ± 1.9 and the observed heterozyosity was averaged at 0.70. All 42 hybrids tested, except for two tissue culture mutants, were uniquely identified with the markers used. Sibling hybrids were closely clustered. Hybrids were also closer to parents. These SSR markers can be used for molecular ecology research, genetic mapping and marker‐assisted breeding. They can also help protection for new Dendrobium varieties.     

Development of simple sequence repeat (SSR) markers for the assessment of gene flow between sea beet (Beta vulgaris ssp. maritima) populations

Molecular markers can be used to estimate gene flow indirectly by monitoring the relative frequency of alleles in adjacent populations. Sea beet (Beta vulgaris ssp. maritima) is a wild plant species found along the coastlines of many European countries and is closely related to cultivated beets. A set of six simple sequence repeat (SSR) markers that are polymorphic in UK populations have been developed for sea beet to assess the problems of indirect measurement of gene flow in these populations.     

Application of simple sequence repeat (SSR) markers for molecular diversity and heterozygosity analysis in maize inbred lines

There is an important role of understanding the genetic diversity among and within inbred lines at the molecular level for maize improvement in different breeding programs. The present study was devoted to estimate the level of genetic diversity among the inbred lines of maize using the simple sequence repeat analysis (SSR). The application of six different SSR markers successfully provided the information on similarity or diversity as well as the heterozygosity of the allelic loci for all the eight inbred line of maize.     

Protease inhibitors of pigeonpea (Cajanus cajan) and its wild relatives

Plant protease inhibitors have been implicated in defense against insect pests. Podborer and pod fly are major pests of developing seeds of pigeonpea ( Cajanus cajan L. Millsp.). Therefore, we studied the presence of protease inhibitors in seeds of pigeonpea and its wild relatives. Seed extracts were analyzed for protease inhibitor activities by caseinolytic assay, and the number of protease inhibitors determined by polyacrylamide gel electrophoresis. Besides trypsin and chymotrypsin inhibitors, seed extracts contained weak papain inhibitor(s) but no bromelain inhibitor. Treatment of seed extract with bromelain generated new active forms of trypsin inhibitors. The relative amounts of different trypsin inhibitors and the total trypsin inhibitor activity varied with different extraction media. Trypsin inhibitors were not detectable in pigeonpea leaves. The profiles of trypsin and chymotrypsin inhibitors in almost all the cultivars of pigeonpea analyzed were similar; however, those in wild relatives were quite variable.     

Biochemical changes in developing seeds of pigeonpea (Cajanus cajan)

Soluble sugars, starch, soluble nitrogen and protein nitrogen were studied in developing seeds of 3 cultivars of pigeonpea. When expressed on a per seed basis soluble sugars increased up to 35 days after flowering and then declined slightly. Rapid starch accumulation was observed between 14 and 28 days after flowering. The levels of soluble nitrogen and protein nitrogen underwent rapid changes during the same period. Amino-acid composition of seed protein was also studied at different stages of maturation. Sodium dodecyl sulphate polyacrylamide gel electrophoresis of salt-soluble proteins revealed that seed storage globulins are formed after 14 days of flowering and do not change much during later stages of maturation.     

Development and use of simple sequence repeat SSR markers in Rubus species

The isolation of polymorphic codominant microsatellite markers in Rubus and in particular red raspberry will provide a tool to investigate gene flow between cultivated and wild raspberries. Microsatellite loci were isolated by screening a PstI size selected genomic library with AC₍₁₃₎ and AG₍₁₃₎. Positive clones were sequenced and primer pairs designed to the sequences flanking identified SSRs. One primer of each pair was fluorescently labelled to facilitate polymerase chain reaction (PCR) product identification on an automated DNA sequencer. We describe 10 polymorphic microsatellite loci developed and demonstrate their usefulness in different Rubus species.     

Tolerance to reniform nematode (Rotylenchulus reniformis) race A in pigeonpea (Cajanus cajan) genotypes

The reniform nematode (Rotylenchulus reniformis) is an important pathogen of pigeonpea (Cajanus cajan). Forty‐six medium maturity (mature in 151–200 days at Patancheru, India) pigeonpea genotypes were evaluated for resistance and tolerance to the reniform nematode in greenhouse and field tests, over the period 1990–97. Each genotype was screened for number of nematode egg masses on a 1 (no egg mass = highly resistant) to 9 (> 50 egg masses = highly susceptible) scale. Plant biomass production in carbofurantreated plots was compared with that in non‐treated plots in a field naturally infested with R. reniformis. Pigeonpea genotypes C 11, ICPL 87119 and ICPL 270 were used as nematode susceptible checks. Genotypes with good plant growth, both in nematode‐free and nematode‐infested plots, were identified as tolerant and evaluated for plant growth and yield for at least three years. All the tested genotypes were susceptible (7 and 9 egg mass score). Single‐plant‐selections, based on plant vigour and yield, were made from genotypes showing tolerance to nematode infection. The level of tolerance was enhanced by plant‐to‐progeny row selection for plant vigour and seed yield in a nematode‐sick field for at least three years. The most promising nematode tolerant genotypes produced significantly greater yield and biomass than the locally grown pigeonpea cultivars in fields naturally infested with R. reniformis at two locations. Pigeonpea landraces are considered to be the most likely sources of tolerance to the nematode. These reniform nematode tolerant lines represent new germplasm and they are available in the genebank of pigeonpea at ICRISAT bearing accession numbers ICP 16329, ICP 16330, ICP 16331, ICP 16332, and ICP 16333.     

Development and characterization of simple sequence repeat DNA markers for Zelkova serrata

We developed 14 microsatellite loci from an enriched genomic DNA library of a broad‐leaved deciduous tree, Zelkova serrata. Of 198 clones from the library, 112 contained microsatellite repeat regions. The M13‐tailed primer method was used for economy. Sequence‐specific primer pairs were designed for 58 of 76 candidate clones. Fourteen of these primer pairs successfully amplified polymorphic single loci among 34 individuals collected from the Kanto breeding region in Japan. The expected heterozygosity for the 14 microsatellite markers ranged from 0.378 to 0.876, suggesting that these will prove valuable for breeding and ecological studies on Z. serrata.     

用SSR标记分析广西香稻与南亚香稻的遗传多样性

利用16对分布于水稻12条染色体上的SSR引物分析78份来自南亚的香稻资源和18份广西种植的香稻的遗传多样性。结果表明:在南亚的香稻资源中,每对引物检测到的等位基因数为3~13个,平均每个位点的等位基因数为5.31个,广西的香稻资源中,每对引物检测到等位基因数2~9个,平均每个位点的等位基因数为3.44个;南亚香稻资源平均多态信息含量(PIC)为0.55,广西香稻资源平均PIC为0.41;南亚香稻资源平均基因多样性(Hs)为0.60,广西香稻资源平均Hs为0.47;说明了南亚香稻资源比广西香稻资源具有更为丰富的遗传多样性。聚类结果表明,大部分的南亚香稻资源或大部分的广西香稻资源各自聚为一类,说明大部分南亚和广西的香稻种质资源存在遗传差异性和地理远缘性。     

Assessment of genetic diversity in broomcorn millet （Panicum miliaceum L.） using SSR markers

The genetic diversity of 118 accessions of broomcom millet （Panicum miliaceum L.）, collected from various ecological areas, was analyzed. Using 46 SSR （Simple Sequence Repeat） polymorphic markers from rice, wheat, oat and barley, a total of 226 alleles were found, which exhibited moderate level of diversity. The number of alleles per primer ranged from two to nine, with an average of 4.91. The range of polymorphism information content （PIC） was 0.2844）.980 （average, 0.793）. The expected heterozygosity （He） varied from 0.346 to 0.989, with an average of 0.834. The average coefficient of the genetic similarity of SSR markers among the 118 accessions was 0.609, and it ranged from 0.461 to 0.851. The UPGMA （Unweight Pair Group Method with Arithmetic Mean） clustering analysis at the genetic similarity value of 0.609 grouped the 118 accessions into five groups. Mantel test meant that geographical origin and genetic distance presented positive correlation. The clustering results were consistent with known information on ecological growing areas. The genetic similarity coefficient of the accessions in the Loess Plateau ecotype was significantly lower than those in the other ecotypes. It indicates that the highest level of genetic diversity occurred in the Loess Plateau, which is probably the original site of Panicum miliaceum.     

Development of simple sequence repeat markers for the plant pathogenic rust fungus,Puccinia graminis

Twenty‐four dinucleotide simple sequence repeat markers were developed for the phytopathogenic fungus, Puccinia graminis. The identified loci were polymorphic, with allelic diversity ranging from two to 11 alleles. Observed and expected levels of heterozygosity ranged from 0.000 to 0.960 and from 0.113 to 0.846, respectively. Fourteen of the loci deviated significantly from Hardy–Weinberg equilibrium. Null alleles were observed for 10 of the 24 loci with a frequency of 4–16%. A preliminary screen of other Puccinia cereal rust fungi (P. coronata, P. striiformis and P. triticina) indicated that these primer pairs are specific to P. graminis.     

Development of simple sequence repeat markers for the plant pathogenic rust fungus Puccinia triticina

Eighteen polymorphic di‐ and trinucleotide simple sequence repeat markers were developed for the phytopathogenic rust fungus Puccinia triticina. The allelic diversity varied from two to nine alleles per locus. Levels of observed heterozygosity ranged from 0.095 to 0.952. Seven of the loci deviated significantly from Hardy–Weinberg equilibrium (P < 0.002) with 70% having levels of observed heterozygosity higher than expected heterozygosity. Null allele(s) were observed for locus PtSSR76 with a frequency of 9%. A preliminary screen of other cereal rust fungi (P. coronata, P. graminis, P. recondita and P. striiformis) indicated that these primer pairs are specific to P. triticina.     

Genetic diversity and origin of weedy rice (Oryza sativa f. spontanea) populations found in North-eastern China revealed by simple sequence repeat (SSR) markers

BACKGROUND AND AIMS: Weedy rice (Oryza sativa f. spontanea) is one of the most notorious weeds occurring in rice-planting areas worldwide. The objectives of this study are to determine the genetic diversity and differentiation of weedy rice populations from Liaoning Province in North-eastern China and to explore the possible origin of these weedy populations by comparing their genetic relationships with rice varieties (O. sativa) and wild rice (O. rufipogon) from different sources. METHODS: Simple sequence repeat (SSR) markers were used to estimate the genetic diversity of 30 weedy rice populations from Liaoning, each containing about 30 individuals, selected rice varieties and wild O. rufipogon. Genetic differentiation and the relationships of weedy rice populations were analysed using cluster analysis (UPGMA) and principle component analysis (PCA). KEY RESULTS: The overall genetic diversity of weedy rice populations from Liaoning was relatively high (H(e) = 0.313, I = 0.572), with about 35 % of the genetic variation found among regions. The Liaoning weedy rice populations were closely related to rice varieties from Liaoning and japonica varieties from other regions but distantly related to indica rice varieties and wild O. rufipogon. CONCLUSIONS: Weedy rice populations from Liaoning are considerably variable genetically and most probably originated from Liaoning rice varieties by mutation and intervarietal hybrids. Recent changes in farming practices and cultivation methods along with less weed management may have promoted the re-emergence and divergence of weedy rice in North-eastern China.     

基于SSR标记的六倍体小黑麦遗传多样性分析

采用已筛选出的多态性较好的分布于六倍体小黑麦21对染色体上的100对SSR引物对从国际玉米小麦改良中心(CIMMYT)引进的339份六倍体小黑麦进行了遗传多样性分析。结果显示,100对引物共检测出323个等位变异,变幅是1~6个,平均等位变异丰富度为3.23;多态信息含量(PIC)的变幅为0~0.748,平均多态信息含量为0.465;平均遗传多样性指数(H')为0.1439,说明供试的339份六倍体小黑麦品种的SSR遗传多样性较为丰富。同时基于Nei's遗传距离对339份材料进行聚类分析,可以将供试材料分为6个类群。其中,第Ⅵ类群与其他类群的遗传距离较大、遗传差异较明显。研究结果为将六倍体小黑麦的优良基因应用于普通小麦的遗传改良提供了理论依据。     

Identification and characterisation of traditional chestnut varieties of southern Spain using morphological and simple sequence repeat (SSRs) markers

The maintenance of plant genetic resources requires the identification of places and agroforestry systems that support high levels of genetic diversity. The aim of this work was to clarify the number and names of chestnut ( Castanea sativa ) cultivars in the south of Spain. Accordingly, 100 grafted chestnut trees corresponding to 34 traditional names were evaluated using 10 qualitative morphological traits and seven simple sequence repeat (SSRs) markers. We identified 38 varieties, 12 in the Huelva region and 26 in Malaga, and synonymies and homonymies were discussed. This work demonstrated that the joint use of morphological traits and SSR markers is an efficient method to evaluate the agrobiodiversity of chestnut in this region. It was also stated that chestnut production in the south of Spain is a traditional system using varieties developed ' in situ '. This constitutes a genuine system of on-farm conservation, which is now threatened. Consequently, adopting strategies for its safeguarding are urgently recommended.     

半野生大豆种质资源SSR位点遗传多样性分析

利用12对SSR引物对67份半野生大豆种质进行了遗传多样性的检测分析,结果表明,12个位点共检测到184个等位基因变异,平均每个位点等位基因数目为15．41个,平均多态性信息量,平均遗传多样性指数,平均遗传距离分别为0．849,0．706,0．118,根据SSR分析结果,按欧式距离将67份半野生大豆种质聚类并划分为5个组群。     

Sex allocation and mating systems in pigeonpea,Cajanus cajan (Fabaceae)

Sex allocation theory predicts that: (1) resources allocated to androecium should decrease with an increase in selfing, (2) a decrease in androecium biomass should be accompanied by an increase in the biomass of pistils, and (3) a decrease in androecium biomass should be coupled with a decrease in flower size, specifically corolla biomass. Another predicted change in reproductive traits associated with variation in selfing concerns seed to ovule ratios, but does not directly stem from sex allocation theory. It has been postulated that seed to ovule ratios should be positively correlated with the amount of selfing. These predictions were tested for six accessions of pigeonpea,Cajanus cajan L., that differed in selfing rates. The results were remarkably in accordance with the predictions. We conclude that sex allocation theory provides a powerful tool to understand the evolution of many reproductive traits in plants.     

Analysis of molecular genetic diversity and population structure in Amaranthus germplasm using SSR markers

We assessed the molecular genetic diversity and population structure of Amaranthus species accessions using 11 simple sequence repeat markers. A total of 122 alleles were detected, and the number of alleles per marker (N_A) ranged from 6 to 21 with an average of 11.1 alleles. The frequency of major alleles per locus ranged from 0.148 to 0.695, with an average value of 0.496 per marker. The overall polymorphic information content values were 0.436–0.898, with an average value of 0.657. The observed heterozygosity (H_O) and expected heterozygosity (H_E) ranged from 0.056 to 0.876 and from 0.480 to 0.907, with average values of 0.287 and 0.698, respectively. The average H_O (0.240) was lower than the H_E and gene flow (Nm), and showed substantial genetic variability among all populations of amaranth accessions. The sample groupings did not strictly follow the geographic affiliations of the accessions. A similar pattern was obtained using model-based structure analysis without grouping by species type. Knowledge of the genetic diversity and population structure of amaranth can be used to select representative genotypes and manage Amaranthus germplasm breeding programs.     

Genetic diversity studies and identification of SSR markers associated with Fusarium wilt (Fusarium udum) resistance in cultivated pigeonpea (Cajanus cajan)

Genetic diversity and identification of simple sequence repeat markers correlated with Fusarium wilt resistance was performed in a set of 36 elite cultivated pigeonpea genotypes differing in levels of resistance to Fusarium wilt. Twenty-four polymorphic sequence repeat markers were screened across these genotypes, and amplified a total of 59 alleles with an average high polymorphic information content value of 0.52. Cluster analysis, done by UPGMA and PCA, grouped the 36 pigeonpea genotypes into two main clusters according to their Fusarium wilt reaction. Based on the Kruskal–Wallis ANOVA and simple regression analysis, six simple sequence repeat markers were found to be significantly associated with Fusarium wilt resistance. The phenotypic variation explained by these markers ranged from 23.7 to 56.4%. The present study helps in finding out feasibility of prescreened SSR markers to be used in genetic diversity analysis and their potential association with disease resistance.