QTL pyramiding for producing nutritious and safe rice grains

正Breeding of rice varieties that are enriched with essential micronutrients and simultaneously have reduced levels of toxic elements in grains is largely unexplored in rice breeding practice. In this issue of JIPB, Liu et al.(2020)developed two rice lines with a low level of cadmium and simultaneously high levels of zinc or selenium accumulation in the grains, thus providing elite genetic materials for breeding rice varieties that are important for addressing mineral malnutrition and ensuring food safety.m entary     

Improving blast resistance of Jin 23B and its hybrid rice by marker-assisted gene pyramiding

Rice blast is one of the most serious diseases in rice (Oryza sativa L.) worldwide. Jin 23B is the maintainer line, a parent for a number of hybrid rice varieties used widely in China. However, Jin 23B is highly susceptible to rice blast. In this study, Pi1, Pi2, and D12 were introgressed to improve the blast resistance of Jin 23B and its derived hybrids, Jinyou 402 and Jinyou 207, by marker-assisted selection (MAS). The improved Jin 23B, which carried single, two, and three genes, were evaluated for their resistance to rice blast using natural inoculation methods in disease nursery of Xianfeng, Hubei, China. The results showed that, the greater the number of genes contained in the improved Jin 23B and hybrids, the higher the resistance to rice blast. Pi1, Pi2, and D12 showed a strong dosage effect on the resistance to blast in the hybrid background during the entire growth duration in the field condition, being very useful for breeding blast-resistant hybrids. The result of examining agronomic traits showed that the improved Jin 23B and its derived hybrid rice were taller than or similar to controls, when there was no disease stress.     

Development of nutritious rice with high zinc/selenium and low cadmium in grains through QTL pyramiding

Enriching zinc (Zn) and selenium (Se) levels, while reducing cadmium (Cd) concentration in rice grains is of great benefit for human diet and health. Large natural variations in grain Zn, Se, and Cd concentrations in different rice accessions enable Zn/Se‐biofortification and Cd‐minimization through molecular breeding. Here, we report the development of new elite varieties by pyramiding major quantitative trait loci (QTLs) that significantly contribute to high Zn/Se and low Cd accumulation in grains. A chromosome segment substitution line CSSL^GCC7 with the PA64s‐derived GCC7 allele in the 93‐11 background, exhibited steadily higher Mn and lower Cd concentrations in grains than those of 93‐11. This elite chromosome segment substitution line (CSSL) was used as the core breeding material to cross with CSSLs harboring other major QTLs for essential mineral elements, especially CSSL^GZC6 for grain Zn concentration and CSSL^GSC5 for grain Se concentration. The CSSL^GCC7+GZC6 and CSSL^GCC7+GSC5 exhibited lower Cd concentration with higher Zn and Se concentrations in grains, respectively. Our study thus provides elite materials for rice breeding targeting high Zn/Se and low Cd concentrations in grains.     

籼稻稻米碾磨与外观品质性状的QTL定位

文章利用籼籼交组合特青/IRBB衍生的重组自交系群体, 在2个环境下对稻米碾磨品质和外观品质进行QTL定位。共计检测到控制稻米碾磨品质的QTL 12个和控制外观品质的QTL 18个, 包括糙米率8个、精米率2个、整精米率2个、粒长7个、粒宽5个和长宽比6个, 这些QTL分布于除第4和12染色体外的其他10条染色体上。其中, 第3染色体涵盖粒形基因GS3的区域对粒长、长宽比、糙米率和整精米率具有较大效应, 其献率分别为56.71%、42.23%、10.05%和4.91%; 第5染色体涵盖粒宽基因GW5的区域对粒宽、长宽比、糙米率和精米率具有较大效应, 表型变异贡献率分别为59.51%、36.68%、19.51%和4.56%。此外, 第6染色体涵盖直链淀粉含量基因Wx的区域对糙米率和精米率具有较小效应。GS3和GW5对糙米率和粒形具有重要作用。     

QTL editing confers opposing yield performance in different rice varieties

Grain yield is one of the most important and complex trait for genetic improvement in crops; it is known to be controlled by a number of genes known as quantitative trait loci(QTLs). In the past decade, many yield-contributing QTLs have been identified in crops.However, it remains unclear whether those QTLs confer the same yield performance in different genetic backgrounds. Here, we performed CRISPR/Cas_9-mediated QTL editing in five widely-cultivated rice varieties and revealed that the same QTL can have diverse, even opposing, effects on grain yield in different genetic backgrounds.     

Improving probiotic spore yield using rice straw hydrolysate

Spore-forming Bacillus sp. has been extensively studied for their probiotic properties. In this study, an acid-treated rice straw hydrolysate was used as carbon source to produce the spores of Bacillus coagulans. The results showed that this hydrolysate significantly improved the spore yield compared with other carbon sources such as glucose. Three significant medium components including rice straw hydrolysate, MnSO₄ and yeast extract were screened by Plackett–Burman design. These significant variables were further optimized by response surface methodology (RSM). The optimal values of the medium components were rice straw hydolysate of 27% (v/v), MnSO₄ of 0·78 g l⁻¹ and yeast extract of 1·2 g l⁻¹. The optimized medium and RSM model for spore production were validated in a 5 l bioreactor. Overall, this sporulation medium containing acid-treated rice straw hydrolysate has a potential to be used in the production of B. coagulans spores.     

染色体工程法聚合小麦优质麦谷蛋白亚基研究

采用小偃6号ID单体材料作为受体,中优6号、安农91168和皖38为5 10亚基的供体进行杂交,F1代田间苗期取根尖进行细胞学检测,孕穗期镜检花粉母细胞选择单体植株,并对其套袋自交。F2代籽粒在室内进行SDS-PAGE电泳筛选14 15和5 10亚基聚合且纯合籽粒,将5 10优质亚基转入当地主要优质源之一的小偃6号,同时将其聚合效率与正常二体杂交F2籽粒分离结果相比较。分析认为单体材料在亚基聚合中,其亚基分离完全符合一对基因的独立遗传,具有较高的选育效率。     

水稻蒸煮品质相关QTL定位及候选基因分析

挖掘与稻米蒸煮品质相关的数量性状基因座(quantitative trait locus, QTL)，分析候选基因，并通过遗传育种手段改良稻米蒸煮品质相关性状，可有效提升稻米的口感。以籼稻华占(Huazhan, HZ)、粳稻热研2号(Nekken2)及由其构建的120个重组自交系(recombinant inbred lines, RILs)群体为实验材料，测定成熟期稻米的糊化温度(gelatinization temperature, GT)、胶稠度(gel consistency, GC)和直链淀粉含量(amylose content, AC)。结合高密度分子遗传图谱进行QTL定位，共检测到26个与稻米蒸煮品质相关的QTLs (糊化温度相关位点1个、胶稠度相关位点13个、直链淀粉含量相关位点12个)，其中最高奇数的可能性(likelihood of odd, LOD)值达30.24。通过实时荧光定量PCR (quantitative real-time polymerase chain reaction, qRT-PCR)分析定位区间内候选基因的表达量，发现6个基因在双亲间的表达量差异显著，推测LOC_Os04g20270和LOC_Os11g40100的高表达可能会极大地提高稻米的胶稠度，而LOC_Os01g04920和LOC_Os02g17500的高表达以及LOC_Os03g02650和LOC_Os05g25840的低表达有助于降低直链淀粉含量。这些结果为培育优质水稻新品种奠定了分子基础，并为揭示稻米蒸煮品质的分子调控机制提供了重要的遗传资源。     

QTL mapping in rice

In the past 10 years, interest in applying the tools of molecular genetics to the problem of increasing world rice production has resulted in the generation of two highly saturated, molecular linkage maps of rice, and the localization of numerous genes and quantitative trait loci (QTLs). Primary studies have identified QTLs associated with disease resistance, abiotic stress tolerance and yield potential of rice in a range of ecosystems. The ability to identify, manipulate and potentially clone individual genes involved in quantitatively inherited characters, combined with the demonstrated conservation of numerous linkage blocks among members of the grass family, emphasizes the contribution of map-based genetic analyses both to applied and to basic crop research.     

Sensitivities of rice grain yield and other panicle characters to late-stage drought stress revealed by phenotypic correlation and QTL analysis

A lowland rice variety (Zhenshan97B) was crossed with an upland variety (IRAT109) to construct a set of recombinant inbred lines (RILs). The population was evaluated under both well-watered (control) and drought-stress (drought) conditions for 2 years. Panicle water potential (PWP), panicle length (PL), grain number per plant (GNP), primary branch number (PBN), second branch number (SBN), spikelet density (SPD), and dry grain weight per plant (DGW) were measured. Phenotypic correlation and path analysis were used to interpret the ranking of importance of other panicle traits to grain yield. Comparison of such rankings under control and drought conditions showed varied responses of panicle traits to drought stress. It was indicated that GNP was an important contributor to DGW under control, and even more important under drought. Thirty-two quantitative trait loci (QTLs) for panicle traits and dry grain weight were identified, with contribution rates ranging from 3.33% to 22.66%. Eleven epistatic QTLs were detected. Cases of collocated QTLs under control and drought were found for PL, SPD, GNP, PBN, and SBN, but not for DGW and PWP. The effectiveness of selection under normal and stressed conditions is discussed.     

A large-effect QTL for rice grain yield under upland drought stress on chromosome 1

Drought is a major abiotic stress factor limiting rice production in rainfed areas. In this study we identified a large-effect quantitative trait locus (QTL) associated with grain yield under stress in five different populations on chromosome 1. The effect of this QTL was further confirmed and characterized in five backcross populations in a total of sixteen stress and non-stress trials during 2006 and 2008. In all the stress trials (eight in total) qDTY1.1 showed strong association with grain yield explaining on average 58% of the genetic variation in the trait. Homozygotes for the tolerant parent allele (Apo) yielded on average 27% more than the susceptible parent allele (IR64) homozygotes. Using an Apo/^3*IR64 population, the peak of this QTL (qDTY1.1) was mapped to an interval between RM486 and RM472 at 162.8?cM at a LOD score of 9.26. qDTY1.1 was strongly associated with plant height in all the environments; this was probably due to the presence of the sd1 locus in this genomic region. In a Vandana/^3*IR64 population segregating for sd1, a strong relation between plant height and yield under stress was observed. The observed relation between increased height and drought tolerance is likely due to tight linkage between qDTY1.1 and sd1 and not due to pleiotrophy of sd1. Thus there is a possibility of combining reduced plant height and drought tolerance in rice. The large and consistent effect of qDTY1.1 across several genetic backgrounds and environments makes it a potential strong candidate for use in molecular breeding of rice for drought tolerance.     

Clustered QTL for source leaf size and yield traits in rice (Oryza sativa L.)

Improvement of plant type plays an important role in super-high yield breeding in rice (Oryza sativa L.). In the present study, a set of backcross recombinant inbred lines derived from a cross of 9311 and Zhenshan97, both elite indica hybrid parents, were developed to identify quantitative trait loci (QTL) for flag leaf size, panicle and yield traits. Forty-seven QTL for 14 traits were detected in common in the two environmental trials, of which nine genomic regions contained clustered QTL affecting plant type traits and yield traits. Four co-localized QTL on chromosomes 1, 6, 7 and 8 involving QTL for flag leaf size (flag leaf length, width and area) contained the QTL for yield traits such as panicle weight (PW) and secondary branch number (SBN), and in all cases alleles from 9311 increased source leaf size and were associated with increased sink size and yield (SBN and PW). Using a subset of overlapping substitution lines for the QTL region on chromosome 1, the QTL were validated and narrowed into a 990?kbp interval (RM3746?CRM10435) with pleiotropic effects on flag leaf size, PW, SBN and spikelet number per panicle. These QTL clusters with large effects on source leaf size and yield-related traits provide good targets for marker-assisted breeding for plant type improvement and high-yield potential in rice.     

Mapping QTL main and interaction influences on milling quality in elite US rice germplasm

Rice (Oryza sativa L.) head-rice yield (HR) is a key export and domestic quality trait whose genetic control is poorly understood. With the goal of identifying genomic regions influencing HR, quantitative-trait-locus (QTL) mapping was carried out for quality-related traits in recombinant inbred lines (RILs) derived from crosses of common parent Cypress, a high-HR US japonica cultivar, with RT0034, a low-HR indica line (129 RILs) and LaGrue, a low-HR japonica cultivar (298 RILs), grown in two US locations in 2005–2007. Early heading increased HR in the Louisiana (LA) but not the Arkansas (AR) location. Fitting QTL-mapping models to separate QTL main and QTL × environment interaction (QEI) effects and identify epistatic interactions revealed six main-effect HR QTLs in the two crosses, at four of which Cypress contributed the increasing allele. Multi-QTL models accounted for 0.36 of genetic and 0.21 of genetic × environment interaction of HR in MY1, and corresponding proportions of 0.25 and 0.37 in MY2. The greater HR advantage of Cypress in LA than in AR corresponded to a genomewide pattern of opposition of HR-increasing QTL effects by AR-specific effects, suggesting a selection strategy for improving this cultivar for AR. Treating year–location combinations as independent environments resulted in underestimation of QEI effects, evidently owing to lower variation among years within location than between location. Identification of robust HR QTLs in elite long-grain germplasm is suggested to require more detailed attention to the interaction of plant and grain development parameters with environmental conditions than has been given to date.     

水稻QTL分析的研究进展

水稻许多重要的性状是由多基因控制的数量性状,经典的数量遗传学只能把数量性状作为一个整体进行研究。近年来．高密度分子标记连锁图的构建和有效的生物统计学方法的发展使人们对数量性状遗传基础的研究出现了革命性的变化。通过对不同群体内的个体或品系的分子标记基因型和表型数据的共分离分析,能对QTL进行检测和定位。本文对QTL定位的原理和方法进行了介绍,从QTL的数目和效应、上位性效应、QTL基因型与环境的互作、相关性状的QTL以及个体发育不同阶段的QTL等方面对水稻QTL分析的研究进展进行了综述。水稻基因组测序计划已经完成,本文还对基因组时代水稻QTL精细定位和克隆的方法进行了探讨,对QTL分析在水稻育种中的应用前景进行了展望。     

Identification, isolation and pyramiding of quantitative trait loci for rice breeding

Many agronomically important traits are governed by several genes known as quantitative trait loci (QTLs). The identification of important, QTL-controlled agricultural traits has been difficult because of their complex inheritance; however, completion of the rice genomic sequence has facilitated the cloning of QTLs and their pyramiding for breeding. Because QTLs are derived from natural variation, the use of a wider range of variations such as that found in wild species is important. In addition, Introgression Lines (ILs) developed from wild species in combination with Marker Assisted Selection should facilitate efficient gene identification. This review describes recent developments in rice QTL analysis including mapping, cloning and pyramiding QTLs.     

Improving the yield and quality of DNA isolated from white-rot fungi

A new simple method used to eliminate polysaccharides that cause problems during DNA isolation was established for 6 different white-rot fungi using 1% hexadecyltrimethylammonium bromide (CTAB) as wash buffer and followed by centrifugation. Variation in the DNA yield and quality was ascertained using precipitating agents, detergents and cell-wall-hydrolyzing chitinase. Considerable amount of exopolysaccharides from fungal biomass was removed with the use of 1% CTAB wash buffer followed by centrifugation. The DNA varied in terms of yield and quality. For the DNA extraction use of 2% SDS in extraction buffer worked best for Pycnoporus cinnabarinus, Cyathus bulleri, Cyathus striatus and Cyathus stercoreus, while 2% CTAB worked best for Phanerochaete chrysosporium and Pleurotus ostreatus. Elimination of phenol and use of absolute ethanol for precipitating DNA resulted in good yield and quality of DNA. This DNA was amenable to restriction endonuclease digestion.     

QTL detection for stover yield and quality traits using two connected populations in high-oil maize

Both yield and quality traits for stover portion were important for forage and biofuel production utility in maize. A high-oil maize inbred GY220 was crossed with two normal-oil dent maize inbred lines 8984 and 8622 to generate two connected F_2:3 populations with 284 and 265 F_2:3 families. Seven yield and quality traits were evaluated under two environments. The variance components of genotype (σ_g²), environment (σ_e²) and genotype × environment interactions (σ_ge²) were all significant for most traits in both populations. Different levels of correlations were observed for all traits. QTL mapping was conducted using composite interval mapping (CIM) for data under each environment and in combined analysis in both populations. Totally, 45 and 42 QTL were detected in the two populations. Only five common QTL across the two populations, and one and three common QTL across the two environments in the two populations were detected, reflecting substantial influence of genetic backgrounds and environments on the results of QTL detection for stover traits. Combined analysis across two environments failed to detect most QTL mapped using individual environmental data in both populations. Few of the detected QTL displayed digenic epistatic interactions. Common QTL among all traits were consistent with their correlations. Some QTL herein have been detected in previous researches, and linked with candidate genes for enzymes postulated to have direct and indirect roles in cell wall components biosynthesis.     

A QTL for rice grain yield in aerobic environments with large effects in three genetic backgrounds

A large-effect QTL associated with grain yield in aerobic environments was identified in three genetic backgrounds, Apo/²*Swarna, Apo/²*IR72, and Vandana/²*IR72, using bulk-segregant analysis (BSA). Apo and Vandana are drought-tolerant aerobic-adapted varieties, while Swarna and IR72 are important lowland rice varieties grown on millions of hectares in Asia but perform poorly in aerobic conditions. Two closely linked rice microsatellite (RM) markers, RM510 and RM19367, located on chromosome 6, were found to be associated with yield under aerobic soil conditions in all three backgrounds. The QTL linked to this marker, qDTY6.1 (DTY, grain yield under drought), was mapped to a 2.2 cM region between RM19367 and RM3805 at a peak LOD score of 32 in the Apo/²*Swarna population. The effect of qDTY6.1 was tested in a total of 20 hydrological environments over a period of five seasons and in five populations in the three genetic backgrounds. In the Apo/²*Swarna population, qDTY6.1 had a large effect on grain yield under favorable aerobic (R ² ≤ 66%) and irrigated lowland (R ² < 39%) conditions but not under drought stress; Apo contributed the favorable allele in all the conditions where an effect was observed. In the Apo/IR72 cross, Apo contributed the favorable allele in almost all the aerobic environments in RIL and BC₁-derived populations. In the Vandana/IR72 RIL and BC₁-derived populations, qDTY6.1 had a strong effect on yield in aerobic drought stress, aerobic non-stress, and irrigated lowland conditions; the Vandana allele was favorable in aerobic environments and the IR72 allele was favorable in irrigated lowland environments. We conclude that qDTY6.1 is a large-effect QTL for rice grain yield under aerobic environments and could potentially be used in molecular breeding of rice for aerobic environments.     

Quantitative trait loci pyramiding for fruit quality traits in tomato

Fruit quality is a major focus for most conventional and innovative tomato breeding strategies, with particular attention being paid to fruit antioxidant compounds. Tomatoes represent a major contribution to dietary nutrition worldwide and a reservoir of diverse antioxidant molecules. In a previous study, we identified two Solanum pennellii introgression lines (IL7-3 and IL12-4) harbouring quantitative trait loci (QTL) that increase the content of ascorbic acid (AsA), phenols and soluble solids (degrees Brix; °Bx) in tomato fruit. The purpose of the present work was to pyramid into cultivated varieties the selected QTL for enhanced antioxidant and °Bx content. To better understand the genetic architecture of each QTL, the two ILs were crossed to the recurrent parent M82 (ILH7-3 and ILH12-4) and between them (ILH7-3+12-4). F1 hybrids (ILH7-3+12-4) were then selfed up to obtain F3 progenies in order to stabilize the favourable traits at the homozygous condition. Species-specific molecular markers were identified for each introgressed region and allowed us to select four F2 genotypes carrying both introgressions at the homozygous condition. The F3 double homozygous plants displayed AsA, total phenols and °Bx content significantly higher than M82. Therefore, they may represent suitable genetic material for breeding schemes aiming to increase antioxidant content in tomato fruit.