Distribution of Protein Bodies and Phytate‐Rich Inclusions in Grain Tissues of Low and High Iron Rice Genotypes

The present study aims to understand whether genotypic differences in grain iron (Fe) concentration in four rice genotypes are related to its association with protein bodies containing phytate‐rich inclusions. Rice genotypes with high and low grain Fe concentrations in unpolished brown rice were grown in a greenhouse at Chiang Mai, Thailand, and grains were harvested at maturity. The presence of protein bodies and phytate‐rich inclusions in rice grain tissues were examined by means of light and transmission electron microscopy (TEM). The composition of mineral elements in different grain tissues was examined using energy dispersive X‐ray microanalysis (EDX) and chemical analysis. The relative distribution pattern of protein bodies in the tissues was similar among the four rice genotypes, which resembled the pattern of grain N concentrations in these tissues. The high grain Fe genotypes (based on brown rice Fe concentration) had more protein bodies containing phytate‐rich inclusions in the embryo and aleurone layer tissues than the low Fe genotypes. Phytate‐rich inclusions were not detected in the endosperm tissues in all genotypes. In conclusion, the presence of protein bodies with phytate‐rich inclusions predominantly in the embryo and aleurone regions of the grain is an important parameter contributing to the variation in brown rice Fe concentration among the genotypes, but not in the white rice (the endosperm). Iron associated with the phytate‐rich inclusions present in the embryo and aleurone layer tissues are largely lost during the polishing process to produce white rice.     

云南地方稻种资源核心种质的微卫星分析

摘要：以来自云南地方稻(Oryza sativa L.)种资源核心种质中的113份材料为研究对象，运用36对微卫星引物，研究了籼(indica )粳( japonica )两个亚种间和云南5个稻作生态区间的遗传多样性分布趋势，并筛选了籼粳亚种、水陆生态型和不同生态区的特异指纹标记。结果表明，粳稻的遗传多样性大于籼稻，遗传分化水平较低；而5个生态区中滇西南水陆稻区遗传多样性最大，遗传分化水平较低；滇东北高原粳稻区的遗传多样性最小。这种遗传多样性的分布趋势与前人在形态和同工酶水平上对云南稻种资源多样性的考察，以及云南地方稻种资源核心种质在形态和同工酶水平上的遗传多样性分布趋势基本一致。另外，在所出现的416个指纹标记中，分别发现籼粳特异指纹标记6个，水陆特异指纹标记15个，不同生态区特异指纹标记3个。初步认为，云南地方稻种资源核心种质代表了云南省地方稻种资源的遗传多样性；从DNA水平上看，云南地方稻种资源的遗传多样性中心在云南省的西南部，粳稻的分化水平低于籼稻。微卫星标记是种质资源遗传多样性检测、分类和生态型确认以及核心种质研究中有用的工具。     

Analysis of genetic diversity in a sweet potato (Ipomoea batatas L.) germplasm collection from Tanzania as revealed by AFLP

Sweet potato (Ipomoea batatas L.) is the fifth most important crop in the developing countries after rice, wheat, maize and cassava. The amplified fragment length polymorphism (AFLP) method was used to study the genetic diversity and relationships of sweet potato accessions in the germplasm collection of Sokoine University of Agriculture, Morogoro and Sugarcane Research Institute, Kibaha, Tanzania. AFLP analysis of 97 sweet potato accessions using ten primer combinations gave a total of 202 clear polymorphic bands. Each one of the 97 sweet potato accessions could be distinguished based on these primer combinations. Estimates of genetic similarities were obtained by the Dice coefficient, and a final dendrogram was constructed with the un-weight pair-group method using arithmetic average. AFLP-based genetic similarity varied from 0.388 to 0.941, with a mean of 0.709. Cluster analysis using genetic similarity divided the accessions into two main groups suggesting that there are genetic relationships among the accessions. Principal Coordinate analysis confirmed the pattern of the cluster analysis. Analysis of molecular variance revealed greater variation within regions (96.19%) than among regions (3.81%). The results from the AFLP analysis revealed a relatively low genetic diversity among the germplasm accessions and the genetic distances between regions were low. A maximally diverse subset of 13 accessions capturing 97% of the molecular markers diversity was identified. We were able to detect duplicates accessions in the germplasm collection using the highly polymorphic markers obtained by AFLP, which were found to be an efficient tool to characterize the genetic diversity and relationships of sweet potato accessions in the germplasm collection in Tanzania.     

Development of an algorithm identifying maximally diverse core collections

The development of a core collection, one which represents the genetic diversity of a crop with minimal redundancy and increases utility of the collection as a whole, is especially important as the funding for germplasm collections decreases. With limited resources, it is difficult to manage large germplasm collections and disperse genetically diverse germplasm to plant breeders. An algorithm was developed to assist in selection of core collections based on estimates of genetic distance. The criteria for selection of the maximum genetically diverse set were based on rankings of genetic distance between an accession with respect to all other accessions. Depending on the size core which a user wished, a zone around each selected accession was determined and no other accession within these limits was selected. The premise for the algorithm was that the genetic variability represented in the core must be representative of the distribution of genetic distances within the population of interest. In the present study, the algorithm was used with RAPD-marker-based estimates of genetic distance for 270 Theobroma cacao L. accessions and 134 Capsicum accessions that chose a set representing 18.5% of the population and representing the breadth of RAPD-based variation.     

非洲栽培稻基因渗入系粒形和剑叶形态性状的QTL定位

非洲栽培稻作为重要的水稻种质资源,其基因渗入系可以为普通栽培稻的遗传背景提供新的有利基因,如果能将这些优良基因引入普通栽培稻中,可为水稻分子设计育种提供新的基因资源。本研究以非洲栽培稻基因渗入系YIL60与轮回亲本中9B(Z9B)杂交衍生的包含188个株系的F₂和F_2:3群体为材料,对粒形性状包括粒长、粒宽、籽粒长宽比、千粒重,剑叶形态性状包括剑叶长、剑叶宽进行数量性状点位(QTL)检测。结果共检测到16个QTL,包括2个粒长QTL、3个粒宽QTL、2个籽粒长宽比QTL、2个千粒重QTL、1个剑叶长QTL、6个剑叶宽QTL,分布于第1、第6、第7、第10和第11号染色体上,贡献率为2.25%~25.64%;有4个多效性QTL区间,有4个QTL qGW7-1、qFLL10、qFLW10、qTGW7在F₂和F_2:3群体中被重复检测到,其中在第7号染色体RM3859-RM3394区间检测到同时控制粒长、粒宽、籽粒长宽比和千粒重的QTL,贡献率最高达17.10%,是一个来源于非洲栽培稻的新粒形QTL。本研究为进一步开展粒形、剑叶形态性状基因的精细定位、克隆和分子标记辅助育种工作奠定了一定的理论基础。     

Patterns of SSR variation in bread wheat (<Emphasis Type="Italic">Triticum aestivum</Emphasis> L.) seeds under ex situ genebank storage and accelerated ageing

Maintaining seed viability and germplasm integrity is a challenging task in conservation of plant genetic resources, as seeds under storage will lose viability and genetic changes will occur. Attempt was made to analyze the patterns of genetic changes in wheat germplasm under ex situ genebank storage and accelerated ageing treatments. A set of 16 naturally aged wheat accessions under ex situ genebank storage since 1994 were sampled. Four recently regenerated wheat accessions were selected, four random seed samples were chosen from each accession, and three of them were exposed to three different accelerated ageing treatments. These 32 seed samples in two germplasm sets displayed a range of germination rates from 4 to 98 %. Thirty-seven microsatellite markers representing 21 wheat chromosomes were applied to screen 12 seeds of each sample and 449 SSR alleles were scored. Large SSR variation was found in each germplasm set. There was 73.1 % of the total SSR variation present among the naturally aged samples and 78.2 % present among the accelerated ageing samples. Several analyses for genetic association consistently revealed no clear genetic separations among samples of high or low germination rates in both germplasm sets. Samples under different accelerated ageing treatments did not show much genetic differentiations from the original sample of each accession. Mantel tests revealed non-significant associations between SSR variability and sample germination rates for both germplasm sets. These findings are useful for understanding seed deterioration under different ageing conditions and suggest that genome-wide SSR variability may not provide sensitive markers for the monitoring of wheat seed viability.     

Nitrogen Fertilizer Increases Seed Protein and Milling Quality of Rice

Rice grain breakage during milling is a problem in many parts of Asia. It has been suggested that nitrogen (N) fertilizer can improve the milling quality of rice. Therefore, this study investigates effects of N fertilization on grain N concentration, endosperm storage protein distribution, and milling quality of rice. Four Thai extra long grain commercial rice cultivars (KDML105, KLG1, PTT1, and CNT1) were grown at Chiang Mai University in the wet season of 2001 with 0 or 120 kg of N/ha at flowering. Anatomical sections showed that there was more storage protein accumulated in the lateral regions of polished grain of high N concentration than in grain of low N concentration. Percent (%) unbroken rice was positively correlated with relative abundance of storage protein in the lateral region of the endosperm in all cultivars. Applying N increased head rice N concentration in all cultivars, whereas % unbroken rice was increased in KLG1 and CNT1. KDML105 cultivar, on the other hand, already had high % unbroken rice and more abundant storage protein in the lateral region with the grain of low N concentration. It is hypothesized that high density of storage protein in the lateral region of the endosperm provides resilience and lessens grain breakage during milling. The additional protein may increase hardness in rice grains and thus could make the rice more resistant to breakage during milling. Furthermore, N fertilization may enhance the nutritional quality of rice grain by increasing the glutelin content, which is rich in lysine.     

Genome-wide association study to identify chromosomal regions related to panicle architecture in rice (Oryza sativa)

Panicle architecture directly affects the grain yield of rice; meanwhile, crop domestication has increased the complexity of rice panicle size and branching pattern. Genome-wide association study (GWAS) was performed to investigate the genetic basis underlying panicle architecture using 183 rice accessions from around the world and a 7 K SNP array. Phenotyping was conducted at Texas A&M AgriLife Research Center in Beaumont, TX. GWAS was performed using MLM (Q?+?K) model using GAPIT software. At p-value?<?0.001, a total of 49 GWAS QTLs controlling various panicle architecture traits were mapped. Considering the recurring and linked SNPs across the panicle architecture traits, 42 independent QTL regions were identified. Among these, 27 QTL regions co-localized with known genes or previously reported QTLs or significant SNP markers, while 15 were potentially novel QTL regions. The results of our study offer useful information on genetic bases controlling panicle architecture in rice, which could be further validated and utilized for designing markers for use in markers assisted selection (MAS) in rice breeding programs.

     

Effect of Grain Morphology on Degree of Milling and Iron Loss in Rice

Grain morphological characteristics were thought to play a significant role in genotypic variation in Fe concentration in white rice. Comparing 17 rice cultivars representing six major grain morphological categories, the present study systematically investigated the relationship between grain morphology, the degree of milling (DOM), and the loss of Fe during the polishing process. The relative importance of key morphological parameters in this relationship was also investigated. The grain morphological characteristics of different rice cultivars significantly affected the degree of Fe loss during polishing to produce white rice. This variation in Fe loss from polishing among the six categories of rice cultivars is mainly due to their difference in DOM (r = 0.73**) and this loss in Fe was the primary factor determining the level of Fe concentration in the white rice. Among the morphological parameters investigated, grain length and length-to-width ratios played the most significant role in determining the DOM, which suggests that these two grain attributes may serve as the initial screening parameters when selecting cultivars for high Fe white rice production. Degree of Fe loss was lowest in short-bold grain shape category compared with the other grain shapes.     

Seed storage protein electrophoresis in Arachis pintoi and A. repens (Leguminosae) for evaluating genetic diversity

Seed storage protein profiles were studied to evaluate the genetic diversity of a germplasm collection of the Caulorrhizae section of genus Arachis. Total seed storage protein of 28 accessions of Arachis pintoi and one of A. repens, collected in the Paranã, São Francisco and Jequitinhonha river basins, was compared by native-PAGE and SDS-PAGE. Significant variation was detected among the protein profiles of different accessions of Arachis pintoi, and three major protein profiles A, B, C were revealed in native-PAGE. Protein variation was much higher between accessions than within accessions. Nevertheless an exceptional case of intra-accession variation was observed in accession W 34b. In SDS-PAGE major variation between the accessions was confined to the region of arachin (basic group), which corresponds to region III in native-PAGE. There was no correlation between seed protein profiles and geographic distribution. However, protein polymorphism is predominantly in accessions of the São Francisco (A, B and C phenotypes) and Paranã (A and B phenotypes) basins, with the B phenotype predominating in the São Francisco basin. A specific protein profile to differentiate between the typical forms of A. pintoi and A. repens was not found.     

The genetic structure and conservation of aus, aman and boro rices from Bangladesh

A diverse set of 115 rice varieties from Bangladesh was surveyed using 35 polymorphic RAPD (randomly amplified polymorphic DNA) markers and the genetic structure of this germplasm, encompassing the principal rice ecotypes of Bangladesh (aus, aman and boro), was determined using multivariate analysis. The level of genetic diversity was evaluated and compared with the levels of diversity found within other rice growing areas of the world. Geographical information systems analysis using Atlas-GIS was employed to analyse and present the geographic distribution of genetic diversity across Bangladesh, and cluster analysis was used to test the efficiency of selection of material for a core collection.     

Genetic variation in cucumber (Cucumis sativus L.) as assessed by random amplified polymorphic DNA1

Isozyme and restriction fragment length polymorphisms (RFLPs) have been applied to studies of genetic relationships and germplasm management in cucumber (Cucumis sativus L.). However, isozymes identify relatively few polymorphisms, and RFLPs are technically complex, expensive, and not compatible for the high through-put required for rigorous assessment of this narrow-based germplasm. Since random amplified polymorphic DNA (RAPD) markers do not manifest such shortcomings, a study was conducted in cucumber to examine genetic relationships in diverse germplasm, assess the usefulness of RAPD markers in distinguishing elite accessions, and compare the relative effectiveness of RAPD markers to that of isozyme and RFLP markers. One hundred and eighteen C. sativus accessions were analyzed using variation at 71 RAPD loci (44 mapped and 27 unmapped). Genetic distances among accessions were estimated using the simple matching coefficient complement, and analyzed using multi-dimensional scaling. Each accession had a unique marker profile, indicating that RAPD analysis was useful in genotypic differentiation. Germplasm grouping patterns were consistent with individual accession origins, theoretical dispersal routes and discriminating morphological characters (i.e., sex expression and fruit length to diameter ratio). Although elite accessions were discriminated by RAPD profiling, their genetic distances were relatively small (between 0.01 and 0.58), indicating limited genetic diversity in this germplasm array. Assessment of a subset of the germplasm array using RAPDs resulted in genetic distance measurements more similar to published genetic distance estimates by RFLP markers (Spearman rank correlation, r_s = 0.7–0.8) than estimates by isozyme markers (r_s = 0.4). Data indicate that RAPD markers have utility for analysis of genetic diversity and germplasm management in cucumber.     

Evaluation of Genetic Diversity of Wild Rice (Oryza rufipogon Griff.) in Myanmar using Simple Sequence Repeats (SSRs)

As a part of an in situ survey of wild rice (Oryza rufipogon Griff.) in Myanmar (Burma), 16 strains of wild rice were collected, and analyzed for allelic diversity over 74 loci with simple sequence repeat (SSR) markers to obtain a basic information for their conservation. Three each of indica and japonica cultivars were added for a comparison. In the six cultivars and 16 strains of wild rice, three to 15 alleles were detected per locus with an average of 7.9. The wild rice revealed a large number of unique alleles throughout their chromosomes with much wider ranges of variation than those detected in the six cultivars of O. sativa L.. The alleles found in the wild rice were classified into those specific to wild rice, common to wild rice and cultivars, and those similar to indica or japonica cultivars. According to the classification, the genotype of each of the 16 strains of wild rice was schematically depicted. The genetic variation among individual strains within a collection site was larger than the variation among the collection sites.     

Exploring genetic diversity and disease response of cultivated rice accessions (<Emphasis Type="Italic">Oryza</Emphasis> spp.) against <Emphasis Type="Italic">Pyricularia oryzae</Emphasis> under rainfed upland conditions in Benin

The main goal of this study is to gain insight into the relationship between the genetic profile of cultivated rice (Oryza spp.) accessions and their resistance to rice blast. Therefore, the genetic and phenotypic variability of a set of 350 cultivated rice accessions originating from Africa (Benin, Mali and Nigeria, Ivory Coast etc.) was examined. Seventy-seven fluorescent amplified fragment polymorphism (AFLP) markers were used to gain insight into the genetic variation and to classify the germplasm collection. In addition, the rice germplasm was assessed for its resistance to blast disease caused by Pyricularia oryzae in upland field conditions. Huge differences in responses of rice accessions to P. oryzae were observed, ranging from highly susceptible to highly resistant. Twelve percent of all accessions were highly resistant to P. oryzae. Based on their AFLP marker profile these highly resistant accessions could be separated from the other accessions. Stepwise regression revealed that the best prediction of the blast resistance level was achieved with a maximum number of 13 AFLP markers. Marker CTA22 was the most important for accurate prediction of blast resistance, this marker was present in all highly resistant accessions. It can be concluded that AFLP markers are a valuable tool to screen rice accessions for their susceptibility towards blast disease and that, based on a subset of markers, it is possible to predict the resistance to rice blast.     

花后增温对双季优质稻产量和品质的影响

为明确未来气候变暖对双季优质稻产量和稻米品质的影响,采用开放式主动增温系统,早稻以金早47(常规籼稻)、两优287(杂交籼稻),晚稻以象牙香珍(常规籼稻)、万象优华占(杂交籼稻)和甬优5550(籼粳杂交稻)为试验材料,研究花后增温对双季优质稻产量和稻米品质的影响。结果表明,花后増温(早稻1.29℃,晚稻1.73℃)对早晚稻产量均无显著影响。增温条件下,早稻加工品质和垩白粒率均无显著变化,垩白度平均提高了16.0%;晚稻糙米率、整精米率、垩白粒率和垩白度分别平均提高了1.8%、3.5%、30.3%和27.2%;早晚稻蛋白质含量平均提高了6.27%,但直链淀粉含量平均降低了3.53%,淀粉颗粒的平均粒径提高了0.09 μm。增温对稻米RVA谱特征值的影响在季别和品种间存在较大变异。综上,花后增温对早晚稻产量无显著影响,有利于改善稻米的加工品质和营养品质,但降低了稻米的外观品质。本研究结果为未来气候变暖下双季优质稻的优质丰产栽培提供了理论依据。     

一个水稻黄绿叶突变体ygl15的鉴定和基因定位

由籼稻品系杂交后代中发现1个黄绿叶突变体,命名为ygl15。为揭示突变体ygl15叶色变异机制,对其进行了表型鉴定和基因定位分析。结果表明,突变体ygl15从苗期开始表现为黄绿叶,叶片中的叶绿素和类胡萝卜素含量较野生型显著下降,并最终导致其农艺性状受到影响,表现为株高、有效穗数、单株总粒数和单株实粒数显著下降,穗长、每穗粒数和结实率的变化不显著,千粒重略有提高;基因表达分析表明,突变体ygl15叶片中,叶绿素合成和光合系统相关的基因表达上调,但血红素合成相关的基因表达下调或不变。遗传分析表明,ygl15的突变表型受1对细胞核隐性基因控制。以突变体ygl15和中花11杂交的F_2群体为定位群体,经过初步定位和精细定位,将ygl15基因定位在水稻第3号染色体上的分子标记M08124～M08175之间,物理距离约79 kb。本研究结果为进一步克隆ygl15突变基因和研究基因功能奠定了一定的理论基础。     

A study of genetic diversity among Indian bread wheat (Triticum aestivum L.) cultivars released during last 100?years

Genetic diversity was examined in a collection of 263 Indian bread wheat (Triticum aestivum L.) cultivars using 90 SSR markers. These cultivars were classified into Group I (pre-green revolution cultivars) and Group II cultivars (post-green revolution cultivars). SSR markers were also classified into Set-I SSRs (42 random genomic SSRs) and Set-II SSRs (48 SSRs associated with QTLs for grain weight). The SSRs belonging to Set-II exhibited relatively low level of polymorphism, suggesting that the SSRs associated with QTL for grain weight in wheat were probably under selection pressure during wheat breeding. AMOVA indicated that proportion of the variation within each of the two groups of cultivars accounted for most (87.59%) of the molecular variance, while the variation between the two groups of cultivars accounted for only 12.41% of the variance. The estimates of the average number of alleles/locus and gene diversity due to each of the two sets of SSRs suggested increase in overall genetic diversity after green revolution in Indian bread wheat cultivars. Differences were also observed in genetic diversity among cultivars from each of the six wheat growing agro-climatic zones of India. However, decade-wise analysis of genetic diversity among the post-green revolution cultivars indicated a progressive decline in genetic diversity, thus suggesting a need for involving diverse exotic, synthetic and winter wheat germplasm in Indian wheat breeding programs.     

Collection of Lupinus angustifolius L. Germplasm and Characterisation of Morphological and Molecular Diversity

Lupinus angustifolius L. is a Mediterranean species, domesticated in the 20th century, representing an important grain legume crop in Australia and other countries. This work is focused on the collection of wild germplasm and on the characterisation of morphological and molecular diversity of germplasm accessions. It reports the collection of 81 wild L. angustifolius accessions from the South and Centre of Portugal, available at the ‘Instituto Superior de Agronomia Gene Bank’, with subsequent morphological and molecular characterisation of a selection of these and other accessions. A multivariate analysis of morphological traits on 88 L. angustifolius accessions (including 59 wild Portuguese accessions, 15 cultivars and 14 breeding lines) showed a cline of variation on wild germplasm, with plants from Southern Portugal characterised by earlier flowering, higher vegetative development and larger seeds. AFLP and ISSR molecular markers grouped modern cultivars as sub-clusters within the wider diversity of wild germplasm, revealing the narrow pool of genetic diversity on which domesticated accessions are based. The importance of preserving, characterising and using wild genetic resources for L. angustifolius crop improvement is outlined by the results obtained.