Crop breeding for salt tolerance in the era of molecular markers and marker‐assisted selection

Crop salt tolerance (ST) is a complex trait affected by numerous genetic and non‐genetic factors, and its improvement via conventional breeding has been slow. Recent advancements in biotechnology have led to the development of more efficient selection tools to substitute phenotype‐based selection systems. Molecular markers associated with genes or quantitative trait loci (QTLs) affecting important traits are identified, which could be used as indirect selection criteria to improve breeding efficiency via marker‐assisted selection (MAS). While the use of MAS for manipulating simple traits has been streamlined in many plant breeding programmes, MAS for improving complex traits seems to be at infancy stage. Numerous QTLs have been reported for ST in different crop species; however, few commercial cultivars or breeding lines with improved ST have been developed via MAS. We review genes and QTLs identified with positive effects on ST in different plant species and discuss the prospects for developing crop ST via MAS. With the current advances in marker technology and a better handling of genotype by environment interaction effects, the utility of MAS for breeding for ST will gain momentum.     

Molecular markers for late blight resistance breeding of potato: an update

Late blight is the most devastating disease of the potato crop that can be effectively managed by growing resistant cultivars. Introgression of resistance (R) genes/quantitative trait loci (QTLs) from the Solanum germplasm into common potato is one of the plausible approaches to breed resistant cultivars. Although the conventional method of breeding will continue to play a primary role in potato improvement, molecular marker technology is becoming one of its integral components. To achieve rapid success, from the past to recent years, several R genes/QTLs that originated from wild/cultivated Solanum species were mapped on the potato genome and a few genes were cloned using molecular approaches. As a result, molecular markers closely linked to resistance genes or QTLs offer a quicker potato breeding option through marker‐assisted selection (MAS). However, limited progress has been achieved so far through MAS in potato breeding. In near future, new resistance genes/QTLs are expected to be discovered from wild Solanum gene pools and linked molecular markers would be available for MAS. This article presents an update on the development of molecular markers linked to late blight resistance genes or QTLs by utilization of Solanum species for MAS in potato.     

陆地棉重组近交系产量及其构成因素的QTL分析

利用爱字棉1517×德州047重组近交系(recombinant inbred lines, RIL)中G6群体构建的SSR遗传连锁图谱及基于混合线性模型的复合区间作图法对QTL进行定位,并对主效QTL,加性×加性上位性QTL及与环境互作效应进行分析,为利用分子聚合方法提高产量提供理论依据。对2006年、2008年以及2009年的产量性状进行分离分析,检测到24个不同年份的主效QTL,其中相关于单株籽棉、单株皮棉、衣分、子指以及单株铃数的分别检测到1个不同年份稳定存在的主效QTL;对3年的产量性状作环境因子联合分析,检测到14个主效QTL,其中6个与环境互作,检测到20对加加上位性QTL,其中7对与环境互作。不同年份检测的稳定且受环境影响小或不受环境影响的与近处标记紧密连锁的主效QTL可用于分子标记辅助选择,以提高育种的效率。     

陆地棉产量相关性状的QTL定位

中棉所28和湘杂棉2号分别是以中棉所12×4133和中棉所12×8891配制而成的两个陆地棉强优势杂交种。以其F₂为作图群体,筛选6000多对SSR引物,利用两群体间27个共有多态位点,通过JoinMap 3.0软件整合了一张包含245个多态位点、全长1847.81 cM的遗传图谱。利用Win QTLCart 2.5复合区间作图法分别对两群体8个产量相关性状在F₂和F_2:3中进行QTL定位,在中棉所28群体多环境平均值的联合分析中检测到16个QTL,三环境分离分析中检测到43个QTL;在湘杂棉2号群体分别检测到20个和66个QTL。在A3、D8、D9等染色体上有QTL成簇分布现象,同时在两个群体中发现一些不受环境影响且稳定遗传的QTL。对考察的8个性状在两个群体中发现12对共有QTL,控制果枝数、衣分和籽指的QTL增效基因位点均来源于共同亲本中棉所12。综合分析推测中棉所12的育种价值主要是通过提高后代的结铃性来实现的。研究结果为棉花产量性状的分子设计育种提供了有用的信息。     

Integrated breeding approaches for improving drought and heat adaptation in chickpea (Cicer arietinum L.)

Chickpea (Cicer arietinum L.) is a dry season food legume largely grown on residual soil moisture after the rainy season. The crop often experiences moisture stress towards end of the crop season (terminal drought). The crop may also face heat stress at the reproductive stage if sowing is delayed. The breeding approaches for improving adaptation to these stresses include the development of varieties with early maturity and enhanced abiotic stress tolerance. Several varieties with improved drought tolerance have been developed by selecting for grain yield under moisture stress conditions. Similarly, selection for pod set in the crop subjected to heat stress during reproductive stage has helped in the development of heat‐tolerant varieties. A genomic region, called QTL‐hotspot, controlling several drought tolerance‐related traits has been introgressed into several popular cultivars using marker‐assisted backcrossing (MABC), and introgression lines giving significantly higher yield than the popular cultivars have been identified. Multiparent advanced generation intercross (MAGIC) approach has been found promising in enhancing genetic recombination and developing lines with enhanced tolerance to terminal drought and heat stresses.     

Genotypic variation for tolerance to phosphorus deficiency in rice and the potential for its exploitation in rice improvement

Deficiency in phosphorus (P) can severely limit rice yields. Developing cultivars with tolerance to P deficiency may represent a more sustainable solution than sole reliance on fertilizer application. To assess genotypic variation for tolerance to P deficiency the P uptake of 30 genotypes was measured on P‐deficient soil. Variation for P uptake was high, ranging from 0.6 to 12.9 mg P/plant. Traditional varieties were superior to modern varieties. A major quantitative trait locus for P uptake had previously been identified in a population developed by crossing the modern variety ‘Nipponbare’ with the P deficiency‐tolerant landrace ‘Kasalath’. This quantitative trait locus was transferred to ‘Nipponbare’ by three backcrosses. Under P deficiency this improved line surpassed ‘Nipponbare’ in P uptake by 170% and in grain yield by 250%. These results show that the genotypic variation for tolerance to P deficiency in rice can be used successfully in rice improvement. By combining high P uptake of the donor variety ‘Kasalath’ with a high harvest‐index characteristic of modern varieties it was possible to more than triple the grain yield of ‘Nipponbare’ under P deficiency.     

Efficient low-cost DNA extraction and multiplex fluorescent PCR method for marker-assisted selection in breeding

Marker‐assisted selection (MAS) is an increasingly important tool in current breeding efforts for improved crop plants and animal breeds. It enables detection of favourable alleles in early developmental stages and thus may result in substantial cost savings. Until now, however, the high costs of the required chemicals and materials, together with the still very labour‐intensive methods, have been an obstacle to widespread application of MAS. A new multiplex‐polymerase chain reaction (PCR)‐based method has been developed for reliable low‐cost, high‐throughput screening. By its use 3366 apple seedlings were screened with an average hands‐on time from DNA extraction to data ready for analysis of < 4 h per 96 plants, and at a cost below US$ 0.5 per marker per plant. Factors that have a strong effect on segregation ratios such as elevated levels of outcrossing are easily detected, as a significant correlation was observed between deviation from expected segregation ratios in some affected markers and the level of outcrossing in a cross. The new method is suitable for many crop species and, provided that suitable buffers are used for DNA extraction, for animals too.     

QTL for maize grain yield identified by QTL mapping in six environments and consensus loci for grain weight detected by meta‐analysis

Grain yield is the most important and complicated trait in maize. In this study, a total of 498 recombinant inbred lines (RIL) derived from a biparental cross of two elite inbred lines, 178 and P53, were grown in six different environments. Quantitative trait locus (QTL) mapping was conducted for three grain yield component traits (100 grain weight, ear weight and kernel weight per plant). Subsequently, meta‐analysis was performed after a comprehensive review of the research on QTL mapping for grain weight (100, 300 and 1000) using BioMercator V4.2. In total, 62 QTLs were identified for 100 grain weight, ear weight and kernel weight per plant in six environments. Forty‐three meta‐QTLs (MQTLs) were detected by meta‐analysis. A total of 13 candidate genes homologous to eight functionally characterized rice genes were found, and four candidate genes were located in the two hot spot regions of MQTL1.5 and MQTL2.3. Our results suggest that the combination of literature collection, meta‐analysis and homologous blast searches can offer abundant information for further fine mapping, marker‐assisted selection (MAS) breeding and map‐based cloning for maize.     

分子标记辅助选择的修饰回交聚合育种方法及其在棉花上的应用

修饰回交育种法是将杂种品系间杂交和回交方法结合起来,用于棉花多个优良性状聚合的育种改良方法。随着分子标记技术日益完善地用于育种的选择中,我们提出了分子标记辅助选择的修饰回交聚合育种方法。它以生产上推广或即将推广的品种为轮回亲本,将修饰回交育种法和分子标记辅助选择育种相结合,同时对轮回亲本的遗传背景和     

Generation mean analysis of phosphorus‐use efficiency in freely nodulating soybean crosses grown in low‐phosphorus soil

Freely nodulating soybean genotypes vary in their phosphorus (P) uptake and P‐use efficiency (PUE) in low‐P soils. Understanding the genetic basis of these genotypes’ performance is essential for effective breeding. To study the inheritance of PUE, we conducted crosses using two high‐PUE genotypes, two moderate‐PUE genotypes and two inefficient‐PUE genotypes, and obtained F₁, F_2, BC₁ and BC₂ populations. The inheritance of PUE was evaluated using a randomized complete block design. A generation mean analysis of phenotypic data showed that PUE was heritable, with complex inheritance patterns and the presence of additive, dominance and epistatic gene effects. Seed P, shoot P, root P, P‐incorporation efficiency and PUE were largely quantitatively inherited traits. There were dominance, additive × additive and dominance × dominance gene effects on PUE, grain yield, shoot dry weight, 100‐seed weight, root dry weight and shoot dry matter per unit P for populations grown under low‐P conditions. Dominance effects were generally greater than additive effects on PUE‐related indices. These PUE indices can be used to select P‐efficient soybean genotypes from segregating populations.     

Molecular characterization and identification of markers associated with yield traits in mulberry using ISSR markers

Mulberry (Morus indica L.) is an important tree crop being exploited for feeding the silk‐producing insect Bombyx mori L. In order to identify parents suitable for breeding to raise high‐yielding varieties for the non‐traditional areas of Kerala, India and also to identify markers associated with leaf yield attributing traits, the present study was undertaken with 44 mulberry genotypes. Variability on morpho‐biometric traits and molecular markers, generated with 12 selected ISSR primers, was estimated. Significant differences between genotypes were observed for all the traits. The dendrogram generated with morpho‐biometric characters clustered the genotypes into three distinct groups and one isolate, while the same using Inter simple sequence repeat (ISSR) markers clustered the genotypes into five groups and six isolates. The greater resolving power of the ISSR markers was evident form the dendrograms. Using step‐wise multiple regression analysis, a number of markers associated with number of branches, total shoot length, leaf weight, internodal distance, leaf chlorophyll, protein, leaf moisture percentage were identified. These markers could be of much use in Marker assisted selection (MAS) breeding programmes in mulberry, especially when no genetic information in terms of linkage maps and Quantitative Trait Locis (QTLs) is available a plant with high heterozygosity and a long juvenile period.     

Genetics,genomics and breeding of groundnut (Arachis hypogaea L.)

Groundnut is an important food and oil crop in the semiarid tropics, contributing to household food consumption and cash income. In Asia and Africa, yields are low attributed to various production constraints. This review paper highlights advances in genetics, genomics and breeding to improve the productivity of groundnut. Genetic studies concerning inheritance, genetic variability and heritability, combining ability and trait correlations have provided a better understanding of the crop's genetics to develop appropriate breeding strategies for target traits. Several improved lines and sources of variability have been identified or developed for various economically important traits through conventional breeding. Significant advances have also been made in groundnut genomics including genome sequencing, marker development and genetic and trait mapping. These advances have led to a better understanding of the groundnut genome, discovery of genes/variants for traits of interest and integration of marker‐assisted breeding for selected traits. The integration of genomic tools into the breeding process accompanied with increased precision of yield trialing and phenotyping will increase the efficiency and enhance the genetic gain for release of improved groundnut varieties.     

不同生态环境下玉米产量性状QTL分析

以玉米（Zea mays L.）自交系黄早四和Mo17为亲本得到的191个F₂单株为作图群体,衍生的184个F_2∶3 家系作为性状评价群体,分析了单株穗数、穗行数、行粒数、百粒重和单株籽粒产量在北京和新疆2个生态环境下的表现和数量性状基因位点的定位结果。QTL检测结果表明,2个环境共检测出47个QTL,分布于除第10染色体以外的9条染色体,其中与单株穗数相关的QTL共10个,可解释的表型变异为5.3%~25.6%;与穗行数相关的QTL共13个,可解释的表型变异为4.5%~23.2%;与行粒数相关的QTL有9个,解释的表型变异为5.4%~13.7%;与百粒重相关的QTL达10个,可解释的表型变异为4.9%~13.3%;与单株籽粒产量相关的QTL有5个,可解释的表型变异为6.1%~35.8 %。大部分产量QTL只在单一环境下被检测到,说明产量相关QTL与环境之间存在明显的互作。表型相关显著的产量性状,它们的QTL容易在相同或相邻标记区间检测到。研究还发现了若干个QTL富集区域,可能是发掘通用QTL的候选位点。     

分子标记辅助选择籼型直立恢复系

直立型密穗基因是水稻中与株型密切相关的基因,对作物高产分子育种有重要应用价值.为了培育直立密穗型的籼稻新品种,本研究以优良籼稻品种东南恢602(弯穗型)做母本,具有直立型密穗基因的近等基因系DW135为父本配置杂交组合.根据直立型密穗基因dep1在第5外显子上碱基缺失,筛选出一个插入缺失长度多态性(Insertion ...     

作物磷效率相关性状的QTL分析研究进展

土壤缺磷是作物生产的主要限制因素之一。利用遗传育种的途径选育磷高效的作物新品种,结合传统的改土施肥方法,是经济、环保地解决土壤缺磷问题的有效措施。数量性状座位(QTL)的定位分析为磷效率的数量性状遗传学研究和磷高效品种的选育提供了有效的手段和途径。本文对近年来利用分子标记对磷效率及其相关性状进行数量性状QTL定位分析的研究成果进行了综述,讨论了作物磷效率遗传改良存在的问题,展望了该领域的发展前景。     

Marker‐assisted backcross breeding for improvement of drought tolerance in bread wheat (Triticum aestivum L. em Thell)

Drought stress is presently a major productivity limiting factor in wheat. This study developed five wheat lines with inbuilt tolerance to drought stress using marker‐assisted backcross breeding (MABB) approach employing three linked quantitative trait loci (QTLs) in an initial population of 516 BC₁F₁ plants. The high‐yielding wheat cultivar ‘HD2733’ grown over last few years extensively in the eastern plains of India is largely sensitive to drought and is used as the recurrent parent. ‘HI1500’ released for water‐limiting conditions and carrying drought‐tolerant QTLs was used as donor parent. MABB lines were advanced using foreground and background selection, coupled with stringent phenotyping. We identified 29 lines that were homozygous for targeted QTLs in different combinations with background recovery range of 89.2%–95.4%. Further evaluation of selected lines for physiological traits and distinctness, uniformity and stability (DUS) characters under rainfed condition identified five potential varieties for national varietal evaluation programme in the zone. The report is first of its kind in implementing known QTLs for the development of drought‐tolerant wheat lines through MABB approach.     

QTL mapping of phosphorus deficiency tolerance in soybean (Glycine max L. Merr.)

Phosphorus (P) deficiency is a major abiotic stress that limits plant growth and crop productivity throughout the world. In the present study, 184 recombinant inbred line (RIL) families developed from soybean varieties Kefeng No. 1 and Nanong 1138-2 were used to identify quantitative trait loci (QTL) associated with P deficiency tolerance. Seven traits of plant height (HT), weight of fresh shoot (FSW), weight of fresh root (FRW), weight of dry root (DRW), length of main root (RL), phosphorus content in leaf (LP), phosphorus content in root (RP), were used as parameters to assess the phosphorus deficiency tolerance. The QTL mapping for the seven traits was performed using the program WinQTLCart. Seven QTLs were detected and mapped on two linkage groups for three traits of weight of fresh shoot, phosphorus contents in leaf and in root. The QTLs that had LOD scores more than three were detected for all of the three traits above. Most of the QTLs explained more than 10% of the total variation. The two QTLs for phosphorus content in leaf explained more than 20% of the total variation, respectively. Five QTLs were mapped on linkage group F2, and two on linkage F1. It was suggested that the genes related to phosphorus deficiency tolerance located on linkage group F in soybean.Contributed equally to this work.     

Genetic regulation of growth and nutrient content under phosphorus deficiency in the wild barley introgression library S42IL

Phosphorus (P) is an important macronutrient required for plant growth and yield formation. Since decades, breeders aim to optimize P efficiency in crops. We studied a set of 47 wild barley (Hordeum vulgare ssp. spontaneum, Hsp) introgression lines (ILs) in hydroponic culture to identify quantitative trait loci (QTLs) improving growth and nutrient content under P deficiency. Applying a mixed model analysis, a total of 91 independent QTLs were located among 39 ILs, of which 64 QTLs displayed trait‐improving Hsp effects. For example, an unknown Hsp allele on barley chromosome 4H increased shoot dry weight under P deficiency in three overlapping ILs by 25.9%. Likewise, an Hsp allele on barley chromosome 6H increased root dry weight under P deficiency in two overlapping ILs by 27.6%. In total, 31 QTLs confirmed Hsp effects already identified in previous field and glasshouse experiments with the same ILs. We conclude that wild barley contains numerous trait‐improving QTL alleles, which are active under P deficiency. In future, the underlying genes can be subjected to cloning and, simultaneously, used in elite barley breeding.     

Genomics,genetics and breeding of tropical legumes for better livelihoods of smallholder farmers

Legumes are important components of sustainable agricultural production, food, nutrition and income systems of developing countries. In spite of their importance, legume crop production is challenged by a number of biotic (diseases and pests) and abiotic stresses (heat, frost, drought and salinity), edaphic factors (associated with soil nutrient deficits) and policy issues (where less emphasis is put on legumes compared to priority starchy staples). Significant research and development work have been done in the past decade on important grain legumes through collaborative bilateral and multilateral projects as well as the CGIAR Research Program on Grain Legumes (CRP‐GL). Through these initiatives, genomic resources and genomic tools such as draft genome sequence, resequencing data, large‐scale genomewide markers, dense genetic maps, quantitative trait loci (QTLs) and diagnostic markers have been developed for further use in multiple genetic and breeding applications. Also, these mega‐initiatives facilitated release of a number of new varieties and also dissemination of on‐the‐shelf varieties to the farmers. More efforts are needed to enhance genetic gains by reducing the time required in cultivar development through integration of genomics‐assisted breeding approaches and rapid generation advancement.     

低磷胁迫下水稻产量性状变化及其QTL定位

为研究低磷胁迫对水稻产量及其构成因素QTL表达的影响, 以耐低磷旱稻IRAT109和磷敏感水稻越富杂交的116个株系的DH群体为材料, 在低磷和正常栽培条件下, 调查了千粒重、结实率、有效穗数、穗粒数及单株产量等性状。结果表明, 结实率、有效穗数和单株产量对低磷胁迫的敏感性较大, 而千粒重、穗粒数对低磷胁迫的敏感性较小。利用水稻分子连锁图中94个RFLP标记和71个SSR标记, 依据以上5性状低磷胁迫下与对照的差值进行QTL定位。共检测出17个QTL, 其中12个对表型变异的贡献率大于10%。3、6和7号染色体上3个标记区域存在QTL成簇分布, 这些高贡献率QTL及成簇分布QTL可作为水稻耐低磷产量性状分子育种的重要候选区域。