Genetic Characterization of Indigenous Rice Varieties in Eastern Himalayan Region of Northeast India

The eastern Himalayan region of Northeast （NE） India is home to a large number of indigenous rice varieties, which are traditionally classified as Oryza sativa subspecies indica, japonica or intermediate types. The classification based on traditional Cheng’s index is often inconclusive due to phenotypic plasticity of morphological characters, which are influenced by environmental conditions. We used molecular markers specific for indica and japonica subspecies to assess the degree of genetic relatedness of indigenous rice varieties in NE India. The results revealed that majority of upland （jum） and glutinous rice varieties, traditionally considered as japonica, were genetically close to the subspecies indica. All varieties of boro ecotype were found to be indica type, and only a few varieties cultivated in lowland and upland areas were japonica type. Some of the lowland varieties of the sali ecotype were intermediate between indica and japonica, and they showed a closer genetic affinity to O. rufipogon.     

Different Aluminum Tolerance among Indica,Japonica and Hybrid Rice Varieties

Hydroponic cultures were conducted to compare the aluminum(Al) tolerance among different rice(Oryza sativa L.) varieties, including indica, japonica and their hybrids. The results showed that the root growth of rice plant was inhibited in different degrees among Al treated varieties. The Al tolerance observed through relative root elongation indicated that five japonica varieties including Longjing 9, Dharial, LGC 1, Ribenyou and Koshihikari were relatively more tolerant than indica varieties. Most indica varieties in this study, such as Aus 373 and 9311(awnless), were sensitive to Al toxicity. The Al tolerance of most progenies from japonica × indica or indica × japonica crosses was constantly consistent with indica parents. The differences of Al tolerance among Longjing 9(japonica), Yangdao 6(indica) and Wuyunjing 7(japonica) were studied. Biomass and the malondial-dehyde content of Yangdao 6 under Al exposure decreased and increased, respectively, while there was no significant effect on those of Longjing 9 and Wuyunjing 7. Remarkable reduction of root activities was observed in all these three rice varieties. Significantly higher Al content in roots was found in Yangdao 6 compared to Longjing 9 or Wuyunjing 7.     

我国常规稻主栽品种的遗传变异分析

 采用40个SSR标记,分析了329份我国近50年来常规稻主栽品种的遗传变异。结果显示,39个SSR标记具有多态性,在多态性位点共检测到223个等位基因,每个位点2～11个,平均57个;平均Nei基因多样性指数（He）为0632。籼粳亚种间的SSR变异差异明显,籼稻平均等位基因数（Na）和Nei基因多样性指数（Na = 54,He = 0440）均高于粳稻品种（Na = 44,He = 0397）。Nei遗传相似系数表明总体样本具有较小的遗传相似度（I = 0366）,而骨干亲本具有较高的遗传相似度（籼:I = 0590;粳:I = 0590）。这导致了籼粳亚种内较高的遗传一致性（籼:I = 0558;粳:I = 0600）。早、中、晚稻各类型遗传相似度差异明显,晚籼和早粳类型具有较高的遗传变异。籼粳稻品种尤其是粳稻的聚类结果显示出较强的季节型和地域特征。这些均提示育种家应选择更广泛的亲本源以拓宽选育品种的遗传基础。     

利用SSR分子标记分析云南陆稻品种遗传多样性

 利用24对SSR引物对云南131个陆稻品种进行遗传多样性分析。共检测到195个等位基因。每个位点的等位基因数平均为8.125个,范围在5(RM55)～13(RM218、RM241)之间;平均表观杂合度为0.0014,平均期望杂合度为0.6545;平均Shannon Weaver指数(I)为1.381;Nei基因多样性指数(H)平均为0.6543,变幅为0.2073(RM235)～0.8689(RM218)。不同地区间陆稻种质资源遗传多样性比较分析表明,滇西南和滇南地区存在丰富的遗传变异,是云南陆稻品种遗传多样性的分布中心。藏缅语族和孟 高棉语族所种植的陆稻品种遗传多样性最丰富。AMOVA分析表明陆稻的遗传变异主要存在于地区内品种间(82%),只有3%遗传变异存在于地区间,品种内的遗传变异占15%。聚类分析显示Nei遗传相似系数为0.22时,云南陆稻品种分为籼粳两个类群,主坐标分析与UPGMA聚类结果基本吻合,并将类群Ⅳ的4个偏籼品种从粳稻类群中重新划归到籼稻类群中,校正了UPGMA聚类的误差,但是不能区分地理组。     

Genetic Structure and Indica/Japonica Component Changes in Major Inbred Rice Varieties in China

We used 39 SSR markers to analyze the genetic structure of 304 major Chinese inbred rice varieties, and to compare changes in the indica or japonica components in these varieties that have been widely cultivated from the 1950s to the 1990s in China. The genetic structure analysis showed that these rice varieties were distinctly divided into two populations, indica and japonica. The sub-structure of indica varieties was more complex than that of japonica ones. Among the various lines, late-season indica and early season japonica varieties had simpler genetic backgrounds. The seasonal ecotypes were not quite consistent with the subtypes of genetic structure. Twelve SSR loci with specific differentiation between indica and japonica were used to calculate the indica/japonica components. The differences in indica/japonica components among the five decades were not significant, except for late-season indica varieties in the 1990s, which had a significantly higher japonica component. These results will help to understand the genetic structure of the major Chinese inbred rice varieties and will be useful for indica-japonica hybrid breeding in China.     

Genetic Diversity of Rice Landraces from Lowland and Upland Accessions of China

Genetic diversity of rice landraces from lowland and upland accessions of China was investigated using 66 polymorphic simple sequence repeat (SSR) markers.The total number of alleles detected from all 324 tested accessions was 555 with an average allele number (Na) of 8.409 per locus,the average effective number of alleles (Ne) of 3.574 and the average Shannon’s information index (I) of 1.378.The genetic diversity was higher for the indica landraces compared to the japonica landraces,and the upland landraces were more genetically diverse than the lowland landraces.The SSR markers,RM72,RM232,RM219,RM241,RM224 and RM3 showed the highest rates of polymorphism and these SSR markers were suitable to assess the genetic diversity of rice germplasm resources.A dendrogram of 324 accessions of lowland and upland landraces showed that all rice accessions were mainly subdivided into two groups,japonica and indica,with some being intermediate.The distribution of lowland and upland landraces among the japonica and indica rice groups was distinct,with obvious differentiation between the lowland and upland landraces in japonica rice,but no such clear distinction in indica rice.     

利用微卫星标记分析浙江省近年来主要水稻品种的遗传多样性

 利用12个DNA微卫星标记分析了浙江省近年来主要的44个常规水稻品种和54个杂交水稻组合,共检测到等位基因68个,每个标记2~10个;带型数共127种,每个标记3~18种;平均多态性频率0.752,变幅为0.567~0905。常规品种和杂交组合均表现为亚种间遗传差异明显、亚种内遗传差异较小,籼型遗传多样性高于粳型。平均遗传相似系数,常规品种籼型为0.672,粳型为0.711,籼粳间为0.103,杂交组合籼型为0.636,粳型为0.669,籼粳间为0.343。聚类分析显示,以遗传相似系数0.618为阈值将常规品种分成6类,以0.601为阈值将杂交组合分成7类,且多数同类型品种或组合聚为同一类。     

Varietal Differences in Photosynthetic Rates in Rice Plants,with Special Reference to the Nitrogen Content of Leaves

Abstract

The photosynthetic rate in the fl ag leaf of rice at the full heading stage was examined in three japonica varieties, Koshihikari, Aikoku and Asanohikari, and the indica high-yielding variety Takanari at the same level of leaf nitrogen. At an ambient CO₂ concentration of 350 µL L-₁, Takanari had a higher photosynthetic rate and stomatal conductance than the japonica varieties when plants were compared at a leaf nitrogen content of approximately 1.5 g m-₂. Stomatal conductance increased considerably with increases in leaf nitrogen content in the japonica varieties. As a result, at a leaf nitrogen content of approximately 2.0 g m-₂, differences in terms of the photosynthetic rate among varieties were small. By contrast, there were no clear varietal differences in Rubisco content at any identical nitrogen content of leaves. We conclude that stomatal conductance is responsible for the varietal differences in photosynthetic rate examined at the same leaf nitrogen content.     

中国常规稻主栽品种的遗传结构及籼粳组分变化

 采用SSR标记分析了304份我国20世纪50-90年代生产上广泛应用的常规稻主栽品种的遗传结构及不同时期籼粳组分的变化。结果显示,我国常规稻主栽品种可明显分为籼、粳两类,籼稻的亚遗传结构比粳稻更为复杂,但晚籼和早粳类型的遗传背景略为单一。早、中、晚各季节类型与遗传结构的分型结果符合度较低。利用12个籼粳分化特异的SSR位点分析各品种的籼粳组分,发现20世纪90年代晚籼类型的粳型组分明显增加,而其他类型不同时期间籼粳组分的差异较小。研究结果对了解我国常规稻品种的遗传结构以及籼粳交育种具有一定的意义。     

Varietal Differences in Biomass Production of Rice Early After Transplanting at Low Temperatures

Abstract

Low temperature decreases biomass production and yield in rice through a number of physiological and morphological changes. We evaluated biomass production in 22 high-yielding genotypes and four commercial japonica cultivars early after transplanting under field conditions for 2 years. The seedlings were transplanted on 30 April or 1 May (early transplanting, ET) and 4 weeks later (late transplanting, LT). The mean air temperature during the 18 days after transplanting in ET was about 4ºC lower than that in LT in both years. The seedling length was greater in high-yielding japonica varieties than in indica genotypes, whereas the seedling character index (SCI), which is the product of plant age in leaf number and the ratio of the seedling weight to its length, was the highest in the indica genotypes. Varietal differences in biomass production were greater in ET than in LT in all rice genotypes. The biomass at 18 days after transplanting was largest in the japonica high-yielding varieties Kusayutaka and Beko-aoba in both ET and LT. The biomass production of the indica genotypes was found to decrease severely after transplanting at low temperatures although the indica genotypes with high SCIs showed faster leaf emergence than the high-yielding japonica varieties. There was a strong positive correlation between the varietal differences in biomass production and shoot length at 18 days after transplanting in ET in both years. Our study suggests that superior shoot elongation in the high-yielding japonica varieties with large biomass allocation to the stems may be advantageous in maintaining biomass productivity at low temperatures.     

我国水稻主栽品种SSR多样性的比较分析

采用40个SSR标记,比较分析了151份20世纪50年代(78份）和近10年（73份）我国常规稻主栽品种的遗传差异,发现有39个标记具有多态性,多态性位点共检测到213个等位基因,每个位点2～11个,平均5.5个;平均Nei基因多样性指数(He)为0.649,范围在0.309（RM174）～0.869（RM418）。籼粳亚种间SSR多样性差异明显,籼稻平均等位基因数（Na）和Nei基因多样性指数（Na = 4.4,He = 0.458）均高于粳稻品种（Na = 4.0,He = 0.395）。比较了78份20世纪50年代与73份近10年水稻主栽品种的遗传多样性,籼、粳亚种表现出相近的变化趋势,即Nei多样性指数和等位基因数20世纪50年代主栽品种高于近10年的。虽然Nei基因多样性指数的变化并不显著（籼稻：z= 1.471,P=0.141;粳稻：z= 1.932,P=0.053）,但等位基因数目的变化达到显著水平（籼稻：z= 2.677,P=0.007;粳稻：z= 3.441,P=0.001）。分子方差分析(AMOVA)表明,遗传变异绝大部分存在于两时期内,尽管时期间平均贡献的遗传变异仅占1.9％,但仍然达到5％的显著水平;籼、粳亚种两时期间平均贡献的遗传变异高于整个分析样本,分别为5.0％和8.2％;籼、粳亚种不同位点的遗传分化程度也各不相同,籼稻和粳稻品种分别有13个（占33.3％）和11个（占28.2％）SSR位点的等位基因在两时期间差异显著,而其余位点的遗传变异则是因时期内品种间的差异引起的。研究表明近10年我国常规稻主栽品种丢失了一部分等位基因,水稻育种仍应加强更广泛的种质亲本的选择。     

云南稻核心种质矿质元素含量及其变种类型

用等离子体原子发射光谱法测定了在云南省新平县同时繁殖的653份云南稻种核心种质糙米中的P、K、Ca、Mg、Fe、Zn、Cu和Mn共8种矿质元素的含量,比较了云南稻种核心种质8种矿质元素含量与变种分类性状间的差异。结果表明高产多抗育种、多样性降低与矿质元素含量的变化密切相关;高产和多抗水稻品种的K、Ca、Mg、Mn含量明显增加,P、Fe、Zn、Cu含量则明显降低,这与水稻矿质营养的遗传和生理机制密切相关。云南稻种核心矿质元素含量存在地带性分布, P、Fe、Zn、Cu含量高低可能与多样性中心有一定联系。核心种质矿质元素高低及其多样性与籼粳关系不大,但在水陆、粘糯、光壳与否、米色、米味、软米与否之间差异明显。这些结果间接支持了“亚洲栽培稻种—籼粳亚种—生态群—生态变种群—品种类型”五级分类系统的生态变种群。     

水稻叶片气孔密度与气体扩散阻力和净光合速率关系的比较研究

 气孔密度和气体扩散阻力存在着极显著的类型间和品种间差异，一般籼稻的气孔密度大于粳稻、气体扩散阻力则小于粳稻。通过籼粳稻杂交育成的品种表现为中间型，气孔密度与气体扩散导度和净光合速率之间呈极显著的正相关，与比叶重呈显著的负相关，与单叶面积的相关不显著。籼稻品种较高的光合速率主要来自其大的气孔密度和低的气体扩散阻力。如果通过籼粳稻杂交将籼稻气孔密度大、气体扩散阻力低的特性与粳稻比叶重大的特点适当结合在一起，将有可能获得较高的净光合速率。     

中国主要稻米的粒型及其品质特性

利用近3年全国各地的籼、粳稻稻谷样品5331份(其中籼稻谷3810份,粳稻谷1521份)的米质数据,对我国目前稻米的粒型及其相关品质进行了研究。结果表明,目前生产上应用的籼稻品种的粒长主要有长粒和中粒两种,粒形则以中粒形为主,细粒形为辅;绝大多数粳稻品种的米粒属短、粗类型。籼稻的粒长、粒形均与其整精米率、垩白度、透明度、直链淀粉含量呈极显著负相关,而与胶稠度呈极显著正相关。粳稻的粒长、粒形与其主要品质指标的相关性相对较弱,且其性质也与籼稻的不尽相同。不同粒长组的平均整精米率也不同,其高低顺序是极短、短、中、长、极长,其中粳稻的极短粒与短粒两个类型间的整精米率无明显差别,但两者的整精米率与中粒的差异极显著;籼稻米各粒长组间整精米率的差异均达极显著水平。对各类稻米的品质进行评价的结果显示,粳稻米总体的品质优于籼稻米,有近半数粳稻品种的米质达到了优质米标准,而籼稻仅有1/4达到优质米标准;籼稻米中,极长粒形及长粒形品种中达优质米标准的比率高于中粒形及短粒形的品种。     

Rice root morphological traits are related to isozyme group and adaptation

Rice accessions from the International Rice Research Institute (IRRI) germplasm bank were evaluated for root traits of 40-day-old plants grown in soil in the greenhouse. The 136 accessions represented six groups defined on the basis of isozyme classification, with isozyme group six further subdivided on the basis of origin and morphology. An additional 28 rice cultivars were evaluated for seminal root xylem vessel diameter when grown in pots in a growth chamber. Rice groups differed in root thickness, root xylem vessel diameter, root:shoot ratio, and patterns of root distribution. Isozyme group 1, which corresponds generally to the indica subspecies, had thin, superficial roots with narrow vessels and a low root:shoot ratio. The other major isozyme group, group 6, comprising japonica types, was characterized by thick roots with wider vessels, a greater proportion of the root weight below 15 cm, and a larger root:shoot ratio. On an average, the bulu and temperate group 6 accessions were similar to the non-bulu types except that their root:shoot ratios and proportion of root weight above 15 cm were more similar to group 1. Group 2, with aus types from South Asia, was characterized by intermediate root thickness, but vertical root distribution and root:shoot ratio were more similar to group 6. The minor isozyme groups 3–5 were represented by few accessions, and in general, they had root thickness and root distribution profiles more similar to group 1 than to group 6. While significant differences were observed among isozyme groups for all the traits under study, there was significant variation within groups and groups overlapped for all traits measured. This study highlights the wide range of variability for constitutive root traits in rice. For example, root thickness ranged from 0.68 to 1.04 mm, seminal root xylem vessel diameters from 30 to 58 μm, root:shoot ratios from 0.05 to 0.21, and accessions had from 44 to 73% of the total root weight concentrated in the surface 15 cm of soil. For the 28 cultivars evaluated, root xylem vessel diameter was highly correlated with reported values of leaf epicuticular wax content (r=0.89). These values indicate the range of genetic variation within the rice genome for root morphological traits.     

水稻对光抑制和除草剂DCMU的耐性及其生理遗传特点（英文）

 以籼稻3037、Palghar和粳稻029、02428及其正反交F₁为材料，探讨水稻籼粳亚种对光抑制和DCMU的耐性及其在杂种F₁中的生理遗传特点。结果表明，亲本及正反交F₁的PSⅡ活性对光抑制和除草剂的耐性基本上是一致的。粳稻大于籼稻，籼粳杂种F₁分别与其母本相似。在育种上选用耐光抑制和DCMU（I₅₀较高）的品种作母本是水稻生理育种中选亲配组的重要着眼点之一。     

中国栽培稻等位酶的遗传结构及地理分布

对我国6330份栽培稻品种进行了5种等位酶12个位点的遗传结构分析,共检测到53个等位基因,平均等位基因数为4.41,多样性指数值为0.269,表明中国栽培稻具有丰富的等位酶遗传多样性。地方农家品种和现代育成品种遗传多样性指数差异不大,但现代育成品种等位基因较少,共有13个稀有等位基因仅存在于地方农家品种中。比较我国六大生态稻区的等位酶分布,发现西南稻区的等位酶基因最为丰富,为我国稻种资源的多样性中心,但华北和华中稻区在某些等位酶基因上的多样性以及某些稀有等位基因的存在暗示着淮河流域和长江流域可能与栽培稻的起源有关。利用等位基因聚类分析基本可以把地方农家品种分成两大类,分别是籼稻和粳稻,籼稻的遗传多样性大于粳稻。籼粳稻在等位酶位点上的差异不仅表现为单个等位基因形式和频率的不同,还表现为多位点非随机组合的遗传差异。     

A Comparative Study of SSR Diversity in Chinese Major Rice Varieties Planted in 1950s and in the Recent Ten Years （1995-2004）

Forty pairs of SSR markers were used to compare the genetic diversity changes in 151 Chinese major rice varieties planted in 1950s and in the recent ten years. Of 40 SSR loci, 39 were found to be polymorphic while one locus (RM479) monomorphic. A total of 213 alleles were identified from the 39 polymorphic loci. The average number of alleles per locus (Na) was of 5.5, ranging from 2 to 11. Nei’s gene diversity index (He) varied drastically among loci from 0.309 at RM174 to 0.869 at RM418, with an average value of 0.649. There existed significant difference in SSR allelic diversity between indica and japonica subspecies, and indica had more variation than japonica both in Na and He. By comparison with the genetic changes in Na and He, it was revealed that the varieties planted in 1950s had more alleles and higher He than those in the recent ten years both for indica and japonica rices. The difference between two subspecies for Na was significant in a tendency over time (indica: z = 2.677, P = 0.007; japonica: z = 3.441, P = 0.001), but not significant for He (indica: z = 1.471, P = 0.141; japonica: z = 1.932, P = 0.053). Analysis of molecular variance (AMOVA) indicated that there existed significant difference (P < 0.05) in genetic variation between the two periods, of which more genetic variation was contributed by indica (Fst = 0.050) and japonica (Fst = 0.082) subsets. Using locus-by-locus AMOVA procedure, significant genetic differentiations were observed in 13 loci (RM21, RM128, RM147, RM169, RM190, RM221, RM231, RM251, RM253, RM317, RM341, RM418, and RM478) for indica varieties and 11 loci (RM101, RM135, RM152, RM159, RM169, RM190, RM251, RM253, RM311, RM418, and RM478) for japonica ones between the two periods. It was found some alleles had been lost in current major rice varieties as comparing with those in 1950s. Therefore, it should be necessary to exploit more alien elite genetic resources for extension of genetic background in current rice breeding program.     

Progressive drought alters architectural and anatomical traits of rice roots

Background

Root architectural and anatomical phenotypes are important for adaptation to drought. Many rice-growing regions face increasing water scarcity. This study describes drought responses of 11 Egyptian rice cultivars with emphasis on plastic root responses that may enhance drought adaptation.

Results

Eleven Egyptian rice cultivars were phenotyped for root architectural and anatomical traits after 6 weeks growth in soil mesocosms under well-watered conditions. Four of these cultivars were more intensively phenotyped under progressive drought stress in mesocosms, using a system where more moisture was available at depth than near the surface. In response to drought stress, all cultivars significantly reduced nodal root number while increasing large lateral root branching density and total lateral root length in the deepest portions of the mesocosm, where moisture was available. Nodal root cross-sectional area, but not stele area, was reduced by drought stress, especially in the basal segments of the root, and the number of late metaxylem vessels was reduced in only one cultivar. Alterations in deposition of lignin were detected by UV illumination from laser ablation tomography, enhanced by digital staining, and confirmed with standard histochemical methods. In well-watered plants, the sclerenchyma and endodermis were heavily lignified, and lignin was also visible throughout the epidermis and cortex. Under drought stress, very little lignin was detected in the outer cell layers and none in the cortex of nodal roots, but lignin deposition was enhanced in the stele. Root anatomical phenes, including cross-section area and metaxylem vessel number and lignin deposition varied dramatically along large lateral root axes under drought stress, with increasing diameter and less lignification of the stele in successive samples taken from the base to the root apex.

Conclusions

Root architectural and anatomical traits varied significantly among a set of Egyptian cultivars. Most traits were plastic, i.e. changed significantly with drought treatment, and, in many cases, plasticity was cultivar-dependent. These phenotypic alterations may function to enhance water uptake efficiency. Increased large lateral root branching in the deep soil should maintain water acquisition, while water transport during drought should be secured with a more extensively lignified stele.

     

水稻籼粳特异性RFLP标记及广亲和品种亲缘关系分析

 应用160个RFLP标记分析了21个水稻广亲和品种6个籼粳测验种，发现其中68个标记可以区分籼粳测验种。21个广亲和品种根据与籼粳测验和共有片段比率的大小 可以分为籼，粳和籼粳中间型三类。68个标记在15个籼粳品种中进一步筛选，得到24个籼粳特异性RFLP标记。它们在亚种内杂交带型相同而亚种产不一样。其中RG358、G318为籼稻专一性探针，在粳稻中表现为零等位。以此24个探针为基础构建了广亲和品品种亲缘关系的树状图。讨论了籼粳特异性RFLP标记在水稻遗传育种实践中的应用。