Exploitation of wild annual Cicer species for widening the gene pool of chickpea cultivars

Introgression of unadapted genes from the wild Cicer species could contribute to the widening of genetic base of important traits such as yield, yield attributes and resistance to major biotic and abiotic stresses. An attempt was made successfully to intercross two wild annual Cicer species with three cultivated chickpea cultivars. Four interspecific cross‐combinations were made, and their true hybridity was ascertained through morphological and molecular markers. These cross‐combinations were also studied for some important quantitative traits under real field conditions. The range, mean and coefficient of variation of agro‐morphological traits were assessed in the parental lines, their F₁ and F₂ generations to determine the extent of variability generated in cultivated chickpea varieties. A high level of heterosis was recorded for number of pods/plant and seed yield/plant in F₁ generation. Three cross‐combinations of ‘Pusa 1103’ × ILWC 46, ‘Pusa 256’ × ILWC 46 and ‘Pusa 256’ × ILWC 239 exhibited substantially higher variability for important yield‐related traits. The present research findings indicate that these wild annual Cicer species can be easily exploited to broaden the genetic base of cultivated gene pool for improving seed yield as well as adaptation.     

Comparative assessment of genetic diversity between wild and cultivated barley using gSSR and EST‐SSR markers

Barley is an economically important cereal crop especially for feed and malt production, but its value as food is increasing due to various health benefits. Wild barley is the progenitor of modern day barley cultivars possessing a rich source of genetic variation for various biotic and abiotic stresses. Species‐specific molecular markers have great potential for efficient introgression of these important traits from wild to cultivated barley. In the present study, 140 microsatellite markers were screened to assess the genetic variation and species‐specific markers between wild and cultivated germplasm. Of these 140, a polymorphic set of 48 genomic (gSSR) and 16 EST‐SSRs amplified a total of 685 alleles. Cluster analysis discriminated all 47 accessions and classified wild and cultivated genotypes into two distinct groups, according to their geographic origin. Our analysis indicated that gSSRs were more informative than EST‐based SSRs. Results from PCoA analysis for species‐specific alleles clearly suggest that wild barley genotypes contain a higher number of unique alleles.     

Potential for wild species in cool season food legume breeding

Wild species which are crossable to cultivated pea, lentil, and chickpea have been collected and are maintained in major germplasm collections throughout the world. Wild species of Vicia crossable to the cultivated faba bean have not been found. The primary, secondary, and tertiary gene pools of the cool season food legumes represent potential genetic diversity that may eventually be exploited in cultivated types to overcome biotic and abiotic stresses. Technical difficulties in obtaining hybrids beyond those within the primary gene pool is a major obstacle. Reproductive isolation, embryo breakdown, hybrid sterility, and limited genetic recombination are major barriers to greater use of wild germplasm. Conventional crossing has been successful in producing interspecific hybrids in Lens, Cicer and Pisum and those hybrids are being evaluated for desired recombinants. In vitro culture of hybrid embryos has been successful in overcoming barriers to wider crosses in Lens. The successful transfer of genes from wide sources to cultivated types can be assisted by repeated backcrossing and selection designed to leave behind undesired traits while transferring genes of interest. Molecular marker assisted selection may become a valuable tool in the future use of wild species. In general, too little is known about the possible genetic variation available in wild species that could be valuable in developing resistance to biotic and abiotic stresses. Current efforts on the use of wide hybridization in the cool season food legumes are reviewed and discussed.     

In vitro techniques for genomic alteration in rice plants

Because of the explosive increase in world population, a sufficient food supply must be achieved by varietal improvement in the major cereal crops including rice. It is expected that new in vitro techniques incombination with conventional breeding methods may effectively raise the yield potential. On the other hand, there are many environmental problems to be solved world-wide such as, global warming, environmental pollution, ecological destruction, reduction in water supplies and so on. Therefore, it is necessary to rapidly develop new varieties for the future combining of higher yield potential with excellent grain quality, and resistance to both biotic and abiotic stresses for the promotion of sustainable agriculture. Although many efforts have been made to introduce useful traits from wild species to cultivated rice via hybridization, it is still difficult to overcome breeding barriers such as cross incompatibility and hybrid sterility and inviability in practical breeding. Now in vitro techniques are going to make it possible to use genetic manipulation and cell culture and fusion techniques to speed up the breeding process. For sustainable agriculture, it is important to utilize the useful genes from alien species. For this purpose, asymmetric protoplast fusions have already been used successfully to transfer disease resistance in Brassica napus. In this experiment, a high level of resistance to the rice blast disease was transferred from wild species through asymmetric fusions. It is also noted that manipulation of cytoplasmic genomes is possible through asymmetric fusions as shown in the induction of new cytoplasmic male sterility (CMS). This revised version was published online in August 2006 with corrections to the Cover Date.     

越冬栽培稻产量性状相关QTL定位

越冬栽培稻是一类能越过自然冷冬季节并在第2年春季萌芽、正常开花结实、收获稻谷的水稻品种。本文通过对越冬栽培稻产量性状QTL分析,明确产量相关性状的遗传规律,旨在进一步解析越冬栽培稻产量性状的遗传机制,为育种创新利用提供理论依据。以3份越冬栽培稻构建的3个半同胞F2群体为材料。各考察15个产量相关性状,利用Excel 2003、GraphPad Prism 5.0和QTL IciMapping 4.10软件分析数据、绘制遗传图谱、定位QTL和联合分析。结果表明,产量性状表型值在3群体中呈连续正态分布,表现为数量性状遗传。共检测到37个QTL和26对上位性QTL,贡献率分别介于2.32%～36.31%和1.04%～2.05%;检测到9个同时影响2个及以上产量性状(一因多效)QTL标记区间;以联合分析检测到13个产量性状相关QTL,其中4个QTL区间与单群体检测QTL区间重叠;越冬栽培稻产量相关性状QTL以加–显性效应遗传为主、上位性遗传效应为辅。本研究将为越冬栽培稻产量相关基因挖掘及育种创新利用奠定基础。     

Wild emmer: genetic resources,gene mapping and potential for wheat improvement

Wild emmer, Triticum dicoccoides, the progenitor of cultivated wheat, harbors rich genetic resources for wheat improvement. They include many agronomic traits such as abiotic stress tolerances (salt, drought and heat), biotic stress tolerances (powdery mildew, rusts, and Fusarium head blight), grain protein quality and quantity, and micronutrient concentrations (Zn, Fe, and Mn). In this review, we summarize (1) traits and controlling genes identified and mapped in T. dicoccoides; and (2) the genes transferred to cultivated wheat from T. dicoccoides. These genes, controlling important agronomic traits such as disease resistance, high protein and micronutrient content, should contribute to wheat production and food nutrition. However, most of the rich genetic reservoir in wild emmer remains untapped, highlighting the need for further exploration and utilization for long-term wheat breeding programs.     

Interspecific and intergeneric hybridization and chromosomal engineering of Brassicaceae crops

In Brassicaceae crop breeding programs, wild relatives have been evaluated as genetic resources to develop new cultivars with biotic and abiotic stress resistance. This has become necessary because of the diversification of ecotypes of diseases and pests, changing food preferences, advances in production technology, the use of new approaches such as in vitro breeding programs, and the need for economical production of F₁ seed. To produce potential new cultivars, interspecific and intergeneric hybridizations have been performed between cultivated species and between cultivated species and their wild relatives. Furthermore, interspecific and intergeneric hybrids have been successfully produced using embryo rescue techniques. In this paper, we review the interspecific and intergeneric incompatibilities between Brassicaceae crops and their wild relatives, and the production, characterization, and improvement of synthetic amphidiploid lines, alien gene introgression lines, alloplasmic lines, monosomic alien chromosome addition lines, and monosomic alien chromosome substitution lines. The goal is to provide useful materials to support practical breeding strategies and to study the genetic effects of individual chromosomes on plant traits, the number of genes that control a trait, their linkage relationships, and genetic improvement in Brassicaceae crops.     

Development and evaluation of chromosome segment substitution lines (CSSLs) carrying chromosome segments derived from Oryza rufipogon in the genetic background of Oryza sativa L.

The wild relatives of rice (Oryza sativa L.) are useful sources of alleles that have evolved to adapt in diverse environments around the world. Oryza rufipogon, the known progenitor of the cultivated rice, harbors genes that have been lost in cultivated varieties through domestication or evolution. This makes O. rufipogon an ideal source of value-added traits that can be utilized to improve the existing rice cultivars. To explore the potential of the rice progenitor as a genetic resource for improving O. sativa, 33 chromosome segment substitution lines (CSSLs) of O. rufipogon (W0106) in the background of the elite japonica cultivar Koshihikari were developed and evaluated for several agronomic traits. Over 90% of the entire genome was introgressed from the donor parent into the CSSLs. A total of 99 putative QTLs were detected, of which 15 were identified as major effective QTLs that have significantly large effects on the traits examined. Among the 15 major effective QTLs, a QTL on chromosome 10 showed a remarkable positive effect on the number of grains per panicle. Comparison of the putative QTLs identified in this study and previous studies indicated a wide genetic diversity between O. rufipogon accessions.     

Comparison among available marker systems for cereal introgression breeding: A practical perspective

Summary There is an increasing amount of public sequence information for the main cultivated cereals, such as wheat and barley. It is not foreseeable that comparable efforts or resources could be devoted to related wild species. However, wild species are interesting sources of genetic variation through introgression breeding. Comparative genomics can be a helpful approach to make use of the available genomic resources. In this context, the potential of the wild barley species Hordeum chilense has been explored in recent years. It exhibits great levels of polymorphism and high crossability with different cereal genera. In addition, interesting biotic and abiotic stress resistance genes, and important quality traits like carotene content and seed storage protein variability shown in the species are also expressed in wheat backgrounds, and are the basis of a breeding program. Different approaches have been undertaken for tagging H. chilense genomic regions in a wheat background. The search for the most suitable DNA marker system started with the development of RAPD and SCAR markers due to a lack of sequence information from the wild species. Transferability of markers from wheat and barley (like STSs or SSRs) have also been useful approximations. More recently, SNP development is being accomplished for the species. In this work, the situation and prospects with the available molecular tools are considered from a practical point of view.     

大豆幼苗根系性状的QTL分析

为研究大豆幼苗期根系性状的遗传规律,以中豆29和中豆32构建的RIL群体为材料,在V2期测定水培幼苗根系性状(主根长、侧根数、根重、根体积和根冠比等)及相关性状(株重、茎叶重和下胚轴重等),以方差分析方法估算遗传参数,并采用复合区间作图法对大豆幼苗期根系等性状进行QTL定位。结果表明,在8个染色体上检测到20个根系及相关性状QTL,其中9个主效QTL位于第11和第14染色体,表型贡献率在10.5%~26.1%之间。在第11和第14染色体上,部分根系性状QTL与地上部性状QTL处于同一位置,其QTL的共位性与形态性状表型相关分析结果一致,反映了根系性状与地上部性状存在一定的关联。     

AB-QTL分析法及在水稻优异基因资源发掘和利用中的应用

野生稻是水稻育种的重要种质资源,在其漫长的进化过程中形成了极其丰富的遗传多样性,具有栽培稻所不具有或己消失了的优良基因。利用分子标记技术从野生稻中发掘有利基因是目前稻种资源研究利用中的重点。由于野生稻总的农艺性状表现劣于栽培稻,在实际研究中受到了许多不利因素（不良农艺性状和不利连锁基因的存在、平衡群体中野生稻种较高的不利基因频率、遗传累赘等）的影响,这对野生稻种资源中优异基因的发掘和利用带来了困难。高代回交QTL分析法（advancedbackcrossQTLanalysis,简称AB-QTL）为实现野生种中有利基因的发掘提供了一个新途径,许多研究表明AB-QTL分析法对野生资源中有利基因的发掘是可行的。本文对AB-QTL分析法的理论基础、特性、渗入系构建及其在野生稻遗传分化和产量基因发掘中的应用进行综述,并就今后的研究重点进行了探讨。     

Introgression of genes for dry matter content from wild cassava species

Cassava cultivars often have poor resistance to biotic stresses and lack good quality traits. Wild species of cultivated crops have frequently been used as an important source of genetic diversity. Cassava breeders are becoming increasingly interested in incorporating genes of wild relatives. In 2000 the International Center for Tropical Agriculture (CIAT) initiated a programme to introgress genes for several root yield and quality traits from wild cassava relatives into its germplasm collection. The objectives of this study were to evaluate one resulting inter-specific cross with high variability for dry matter content (DMC) and to assess the effect of such a cross on other yield related traits. Crossing of the elite cultivar MTAI 8 to the wild relative Manihot tristis increased the percentage DMC above the normal average of about 35%, with percentage DMC ranging from 34.39 to 42.73. The crosses, however, were accompanied by some detrimental effects, most noticeable the reduction in harvest index (HI). It is apparent that when selecting for DMC, caution should be taken and HI and fresh root yield should be monitored. Regression analysis singled root weight, percentage DMC and fresh root yield out as the most important contributors to dry root yield. Principal component analysis indicated that root weight, roots per plants and DMC contributed most to storage root yield.     

东乡野生稻抗褐飞虱QTL分析

野生稻是水稻抗褐飞虱基因的重要种质资源。应用东乡野生稻与栽培稻协青早B构建的2套材料,开展水稻抗褐飞虱基因鉴定研究。先以协青早B//协青早B/东乡野生稻BC₁F₅群体为材料,应用褐飞虱田间种群进行抗虫鉴定,检测到2个抗褐飞虱QTL,其中,qBph2位于水稻第2染色体RM29–RG157区间,东乡野生稻等位基因可降低死苗率22.2%;qBph7位于第7染色体RM11–RM234区间,东乡野生稻等位基因可降低死苗率43.7%。进一步以协青早B为轮回亲本,构建了BC₃F₃群体,应用褐飞虱生物型I、II和III进行抗虫鉴定,QTL分析表明qBph2抗褐飞虱生物型I和II,qBph7抗褐飞虱生物型I和III。这2个QTL对培育抗褐飞虱水稻品种具有重要应用价值。     

野生稻种资源的研究与利用动态

从野生稻的种质资源概况、野生稻所具的优良性状、野生稻与栽培稻的亲缘关系、及其在常规育种、杂交育种、生物技术上应用等方面论述野生稻种资源近年来的研究状况,并提出应加强对野生稻中优良基因的分子遗传学研究,促进其在水稻超高产育种、分子育种等方面的应用。     

Detection of exotic QTLs controlling nitrogen stress tolerance among wild barley introgression lines

Nitrogen (N) is one of the most important plant nutrients, controlling growth and, ultimately, yield of a cultivar. Hordeum vulgare ssp. spontaneum, the wild barley progenitor of cultivated barley, is known to possess genes that can improve tolerance against biotic and abiotic stresses. A quantitative trait locus (QTL) study with two levels of N fertilization was conducted under glasshouse in order to locate wild barley alleles that improve N stress tolerance in the genetic background of an elite barley cultivar. For this, a set of 28 barley introgression lines (S42ILs), which originate from the cross ??Scarlett???×???ISR42-8??, was studied. The S42ILs, containing single or multiple wild barley introgressions, and ??Scarlett?? were evaluated in regard to a total of 15 traits, related to morphological parameters, grain parameters as well as to carbon (C) and N content parameters. A mixed model analysis and a subsequent Dunnett test was conducted to identify S42ILs that significantly deviate from the recurrent parent ??Scarlett??, either tested separately for each N level, or simultaneously across both N levels. In total, 65 QTLs were detected for the S42IL set. Most QTLs were found for chlorophyll content during heading (10 QTLs) and the fewest for C/N ratio of straw (1 QTL). The individual S42ILs possessed different numbers of QTLs. For S42IL-108, a maximum of eight QTLs were found whereas S42IL-145 did not show any significant difference from ??Scarlett??. Wild barley alleles revealed decreasing effects at 32 QTLs and increasing effects at 33 QTLs. Although 25 QTLs exhibited similar effects across both N levels, 18 and 22 QTLs exhibited effects that were only detected under N0 or N1, respectively. We, thus, conclude that it may be worth to select improved barley cultivars for N stress tolerance separately under low N fertilization, rather than extrapolating trait performances from experiments carried out under standard N fertilization conditions. A number of wild barley QTL alleles improved N stress tolerance. For example, a wild barley QTL allele on chromosome 4H, present in the Hsp introgression of S42IL-119, was associated with a 13.0?% increase of thousand grain weight across both N levels and a 20?% increase under low N supply. QTLs detected in the present study were compared with those of previous field studies of the same cross and with other QTL studies in barley and other small grains. Accordance between QTL studies (QTLs showing similar effects at the same map location) is documented and discussed. Based on our study, promising wild barley QTL alleles are available in S42ILs, which can be readily utilized to select for improved N use efficiency in barley breeding.     

Genetic Advances in Adapting Rice to a Rapidly Changing Climate

Rice, with its wide geographic distribution extending from 50°N to 35°S, is expected to be the most vulnerable cultivated crop to future changing climates. Among the different abiotic stresses, extreme temperatures coinciding with critical developmental stages, increasingly frequent floods and drought spells, and worsening sea water inundation are some of the major threats to sustainable rice productivity. Following the successful implementation of molecular marker‐assisted backcrossing to introgress large‐effect QTL for submergence tolerance in rice mega varieties, rice breeding for drought, salinity and, recently, heat tolerance is employing the same approach. Although tolerance for combined submergence and salinity has been achieved, developing rice varieties with multiple tolerance for other abiotic and biotic stresses and finding the appropriate agronomic package to exploit their performance remain a challenge. The major bottleneck is the lack of unidentified large‐effect QTL for other abiotic stresses that are strongly influenced by genotype × environment (G × E) interaction. Rapid advances in the use of molecular tools, including a plethora of SNP markers, are expected to facilitate the development of major abiotic stress‐tolerant rice. In response to the actual farmer field situation, progress achieved in understanding and developing independent abiotic stress tolerance is being exploited to combine tolerances (for example, heat and drought; salinity and submergence) to address emerging environmental problems across a wide range of rice ecosystems.     

Comparative fine mapping of fruit quality QTLs on chromosome 4 introgressions derived from two wild tomato species

Despite their unsuitability for agricultural production, the wild relatives of crop species represent a largely untapped resource of novel QTLs potentially useful for crop plant improvement. In this regard, previous introgression studies, involving several different wild tomato species, have shown that the long arm of chromosome 4 contains QTLs for many horticulturally important traits including soluble solids content, fruit shape, lycopene content and biochemical composition. However, these earlier studies were unable to determine how many genes control these traits and whether genes affecting the same character from different wild species are allelic or not. In an effort to shed light on these issues,we have constructed a series of lines containing small, overlapping introgressions for portions of the long arm of chromosome 4 from L. peruvianum and L. hirsutum and tested these lines in replicated field trials. The results provide evidence for multiple, non-allelic loci controlling soluble solids and fruit weight. They also show that the loci controlling some traits (e.g. fruit shape, fruit weight, epidermal reticulation) co-localize to the same portions of chromosome 4, a result that maybe attributed to pleiotropy and/or gene dense areas with lower than average recombination. The implications of these finding for molecular breeding and utilization of exotic germplasm are discussed. This revised version was published online in July 2006 with corrections to the Cover Date.     

水稻染色体片段代换系对氮、磷胁迫反应差异及其QTL分析

利用来源于9311(籼稻)与日本晴(粳稻)杂交后代衍生的遗传背景为9311的染色体片段代换系群体,分析其在大田正常、低氮和低磷条件下的单株有效穗和单株产量的差异。结果表明,低磷、低氮胁迫对单株有效穗和单株产量影响较大。代换系对低磷和低氮的反应存在明显差异。在低氮(磷)水平下共检测到26个单株有效穗和单株产量片段或QTL,以及12个相对单株有效穗和相对单株产量QTL。源于日本晴的等位基因均呈减效作用。低磷和低氮下共同检测到5个导入片段影响单株有效穗或单株产量。而大部分(约81%)QTL只在单胁迫处理下被检测到。表明水稻对磷胁迫和氮胁迫的反应既存在不同的遗传基础,也存在共同的遗传机制。     

Effect of quantitative trait loci for seed shattering on abscission layer formation in Asian wild rice Oryza rufipogon

Asian cultivated rice Oryza sativa L. was domesticated from its wild ancestor, O. rufipogon. During domestication, the cultivated rice lost its seed-shattering behaviour. Previous studies have shown that two major quantitative trait loci (QTLs; qSH1 and sh4) are responsible for the seed-shattering degree. Here, we produced introgression lines carrying non-functional alleles from O. sativa ‘Nipponbare’ at the two major QTLs in the genetic background of wild rice O. rufipogon W630, and examined the effects of the two QTLs on seed shattering and abscission layer formation. The introgression lines, with Nipponbare alleles at either or both loci, showed complete or partial abscission layer formation, respectively, indicating that other unknown loci might be involved in enhancing seed shattering in wild rice. We detected a single QTL named qSH3 regulating seed-shattering degree using an F₂ population between Nipponbare and the introgression line carrying Nipponbare alleles at the two QTLs. Although we generated an introgression line for qSH3 alone, no effects on seed shattering were observed. However, a significant effect on seed-shattering degree was observed for the introgression line carrying Nipponbare alleles at qSH3 and the two QTLs, suggesting an important role of qSH3 on seed shattering in coordination with the two QTLs.     

利用东乡普通野生稻染色体片段置换系定位产量相关性状QTL

以东乡普通野生稻和日本晴为亲本构建的染色体片段置换系为研究材料, 2019年分别在北京、山东临沂和江西南昌对分蘖数、穗粒数和粒形等11个产量相关性状进行多环境鉴定,结合染色体片段置换系基因型数据定位水稻产量相关性状QTL。3个环境共检测到68个QTL,包括株高4个、穗长5个、分蘖数2个、一次枝梗数7个、一次枝梗粒数8个、二次枝梗数8个、二次枝梗粒数10个、每穗粒数6个、千粒重7个、粒长8个和粒宽3个; LOD值介于2.50～12.66之间,贡献率变幅为4.67%～27.79%,15个QTL的贡献率大于15%;24个QTL与已报道位点/基因位置重叠,44个QTL为新发现位点; 6个QTL在2个环境能被检测到, 1个QTL qTGW2能在3个环境检测到,且是还未报道的新位点。最后,利用BSA法验证了qPH7、qPBPP8-2和qGW10三个QTL的可靠性。本研究将为后续产量相关性状基因克隆以及进一步解析其遗传基础和分子调控机制奠定基础。