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Refining the major-effect QTL and candidate genes associated with grain number per panicle by QTL-seq in rice (Oryza sativa L.) 通过QTL-seq分析水稻(Oryza sativa L.)中与每粒粒数相关的主要效应QTL和候选基因
IF 1.9 3区 农林科学 Q2 AGRONOMY Pub Date : 2024-09-12 DOI: 10.1007/s10681-024-03410-6
Gunasekaran Ariharasutharsan, Adhimoolam Karthikeyan, Seshadri Geetha, Ramasamy Saraswathi, Muthurajan Raveendran, Karuppasamy Krishna-Surendar, Latha-Devi Ananda-Lekshmi, Amudha Kailappan, Ramalingam Suresh, Natarajan Devasena

Rice grain yield is a major focus of rice breeding, and with grain number per panicle being a major trait that largely determines overall grain yield. Despite its importance, the genetic architecture and underlying mechanisms governing grain number per panicle are not well understood. In this study, we adopted a whole-genome resequencing-based QTL-seq analysis to trace genomic regions related with grain number per panicle using a mapping population derived from a cross between CB12132 (High grain number) and IET28835 (Low grain number). This approach revealed five candidate genomic regions: qGNPP1.1 (10.40 Mb to 12.76 Mb), qGNPP1.2 (24.61 Mb to 25.33 Mb), qGNPP1.3 (26.57 Mb to 27.26 Mb), qGNPP4.1 (27.70 Mb to 31.34 Mb), and qGNPP5.1 (2.12 Mb to 5.50 Mb) on chromosomes 1, 4, and 5, respectively. Further, we searched for possible candidate genes using a comprehensive approach that included the analysis of gene sequences, functional annotation, and expression patterns. A total of 23 candidate genes, including most possible genes Os01g0292900 (SPL1), Os01g0622000 (OsCUGT1), Os01g0655300 (SDG705), Os04g0615000 (NAL1), Os04g0559800 (SMG2) and Os05g0155200 (ERS2), were identified across the five candidate genomic regions. Collectively, our study results shed light on the genetic mechanisms underlying grain number per panicle in rice and will be helpful for improving grain yield in future rice breeding programs.

水稻籽粒产量是水稻育种的一个重点,而每穗粒数则是在很大程度上决定整体籽粒产量的一个主要性状。尽管每穗粒数非常重要,但人们对其遗传结构和内在机制还不甚了解。在本研究中,我们采用了基于全基因组重测序的 QTL-seq 分析方法,利用 CB12132(高粒数)和 IET28835(低粒数)杂交产生的制图群体,追踪与每穗粒数有关的基因组区域。这一方法发现了五个候选基因组区域:qGNPP1.1(10.40 Mb 至 12.76 Mb)、qGNPP1.2(24.61 Mb 至 25.33 Mb)、qGNPP1.3(26.57 Mb 至 27.26 Mb)、qGNPP4.1(27.70 Mb 至 31.34 Mb)和 qGNPP5.1(2.12 Mb 至 5.50 Mb),分别位于 1、4 和 5 号染色体上。此外,我们还采用包括基因序列分析、功能注释和表达模式分析在内的综合方法寻找可能的候选基因。在五个候选基因组区域中共发现了 23 个候选基因,包括大多数可能的基因 Os01g0292900 (SPL1)、Os01g0622000 (OsCUGT1)、Os01g0655300 (SDG705)、Os04g0615000 (NAL1)、Os04g0559800 (SMG2) 和 Os05g0155200 (ERS2)。总之,我们的研究结果揭示了水稻每穗粒数的遗传机制,将有助于在未来的水稻育种计划中提高谷物产量。
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引用次数: 0
Breeding for resistance to bacterial wilt in Solanaceae crops: lessons learned and ways forward for Gboma eggplant (Solanum macrocarpon L.), a traditional African vegetable 茄科作物抗细菌性枯萎病的育种:非洲传统蔬菜 Gboma 茄子(Solanum macrocarpon L.)的经验教训和前进方向
IF 1.9 3区 农林科学 Q2 AGRONOMY Pub Date : 2024-09-11 DOI: 10.1007/s10681-024-03393-4
Belchrist E. Sossou, Mathieu A. T. Ayenan, Roland Schafleitner, Sikirou Rachidatou, Enoch G. Achigan-Dako

Bacterial wilt (BW) is caused by Ralstonia solanacearum species complex (RSSC) and can lead to severe losses in a wide range of crops, including many traditional African vegetables (TAV). Given the critical role of TAV in African food security, investigations of BW incidence, distribution, and effective breeding strategies are needed to support public and private TAV breeding programs. In this review, we address key questions related to the diversity of BW pathogens, susceptible TAV hosts, distribution, incidence, breeding strategies, sources of resistance, and gaps in the development of resistant TAV varieties in Africa. We also discuss the potential of multiomics integration to enhance our understanding of the host plant defense system against BW in Solanaceae crops. We curated BW strain databases obtained from several online platforms, representing a total of 948 BW strains. Using a refined database, we highlighted the diversity of RSSC and TAV crops affected by RSSC in different regions of Africa. Out of 29 species documented to be affected by BW in Africa, ten are TAV, including widely consumed TAV such as Amaranths and nightshades. In addition, phylotypes I and III are reported to affect TAV, and the incidence can reach up to 72.4% in farmers’ fields. An overview of the first reports revealed that the disease has become a serious threat to TAV in the past decade. Finally, this review proposes a schematic map of possible avenues for successful breeding of BW-resistant TAV using Gboma eggplant as a case study.

细菌性枯萎病(BW)是由茄属拉氏菌(Ralstonia solanacearum)复合菌种(RSSC)引起的,可导致包括许多传统非洲蔬菜(TAV)在内的多种作物遭受严重损失。鉴于非洲传统蔬菜在非洲粮食安全中的关键作用,我们需要对BW的发病率、分布和有效的育种策略进行调查,以支持公共和私人的非洲传统蔬菜育种计划。在这篇综述中,我们探讨了与 BW 病原体多样性、易感 TAV 宿主、分布、发病率、育种策略、抗性来源以及非洲抗性 TAV 品种开发方面的差距有关的关键问题。我们还讨论了多组学整合的潜力,以加强我们对茄科作物宿主植物防御系统的了解。我们整理了从多个在线平台获得的 BW 菌株数据库,共包含 948 个 BW 菌株。利用完善的数据库,我们突出了非洲不同地区受 RSSC 影响的 RSSC 和 TAV 作物的多样性。在记录的非洲受 BW 影响的 29 种作物中,有 10 种是 TAV,包括广泛食用的 TAV,如苋菜和夜来香。此外,据报告,噬菌体 I 型和 III 型也会影响 TAV,在农田中的发病率可高达 72.4%。对最初报告的综述显示,在过去十年中,该疾病已成为对 TAV 的严重威胁。最后,本综述以 Gboma 茄子为例,提出了成功培育抗 BW TAV 的可能途径示意图。
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引用次数: 0
Early sex identification by leaflet distance in plantlets of Cycas revoluta 通过苏铁小叶距离识别早期性别
IF 1.9 3区 农林科学 Q2 AGRONOMY Pub Date : 2024-09-10 DOI: 10.1007/s10681-024-03407-1
Ylenia De Luca, Salvatore Cozzolino, Antonia Cristaudo, Alex Widmer, Donata Cafasso

In dioecious plants, the process of sex determination usually occurs during the reproductive stage. However, it can be challenging to determine the sex of long-lived plants with long generation times. This is true for Cycas revoluta, which produces toxic seeds in female plants, leading to a preference for male plants in public green spaces. In this study we aim to identify a morphological trait that can be used to distinguish between the sexes in C. revoluta at a very early stage of plant growth. We sampled C. revoluta seedlings/plantlets at three different early growth stages and identified the sex of individuals by PCR amplification of a male-specific molecular marker. On the same plants, we measured morphological traits, including the distance between leaflets on the leaf rachis, perimeter, area, number of indents, and leaf complexity, and evaluated their correlation with the sex of the individuals. Among all measured traits, the medium distance between leaflets on the leaf rachis was found to be a sexually dimorphic morphological trait in Cycas plantlets in all three growth stages. In particular, the distance between leaflets on the leaf rachis in the upper part of the leaf in the first stage revealed no overlap between the sexes. Whenever available, morphological traits for sex differentiation in greenhouses and plant nurseries can represent a rapid and economic tool when coupled with automatized image recognition systems.

在雌雄异体植物中,性别鉴定过程通常发生在生殖阶段。不过,要确定世代时间长的长寿植物的性别可能很困难。苏铁(Cycas revoluta)就是如此,它的雌株会结出有毒的种子,导致人们在公共绿地上偏爱雄株。在本研究中,我们旨在确定一种形态特征,用于在植物生长的早期阶段区分苏铁的性别。我们在三个不同的早期生长阶段对 C. revoluta 的幼苗/小植株进行了取样,并通过 PCR 扩增雄性特异性分子标记来确定个体的性别。在相同的植株上,我们测量了形态特征,包括叶轴上小叶之间的距离、周长、面积、压痕数和叶片复杂度,并评估了它们与个体性别的相关性。在所有测量的性状中,发现叶轴上小叶之间的中等距离是苏铁小株在所有三个生长阶段的性别二态形态性状。尤其是第一阶段叶片上部叶轴上小叶之间的距离在两性之间没有重叠。只要有可用的形态特征,在温室和苗圃中进行性别区分时,与自动化图像识别系统结合使用可成为一种快速、经济的工具。
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引用次数: 0
QTL mapping and epistatic interactions for improved seed oil quality in safflower 红花种子油质改良的 QTL 图谱和表观相互作用
IF 1.9 3区 农林科学 Q2 AGRONOMY Pub Date : 2024-09-10 DOI: 10.1007/s10681-024-03408-0
Seyedeh Esmat Hashemi, Nafiseh Mahdi Nezhad, Ghasem Mohammadi-Nejad, Fatemeh Ebrahimi, Barat Ali Fakheri

Safflower oil with high oleic is an important source of oil due to its oxidative stability and nutritional value as well as its industrial benefits.

Identification of molecular markers associated with oil quality traits may aid in genotype selection in breeding efforts of safflower. To determine the genetic basis of seed oil, oleic acid, and linoleic acid content in safflower seeds, a recombinant inbred population was developed from a cross between Goldasht (low oleic line) and Mex 22–191 (high oleic line) by individual self-pollinated plants in each generation (from F2 to F9). Fatty acid components were detected by gas chromatography and subsequently analyzed by QTL analysis. The high variability in fatty acid composition was demonstrated and the first high-oleic safflower genotype was generated. A new linkage map with 69 AFLP and 45 ISSR polymorphic markers was made, covering 1472,441 cM of the safflower genome. A total of 63 individual QTLs and 238 epistatic QTLs, related to oil quality, were detected in 14 genomic regions. Some major QTLs with phenotypic variation greater than 10% were identified for the measured traits. These results demonstrate that major QTL may play an important role in increase the oleic acid of the genetic material used. Furthermore, the larger number of minor QTLs and epistatic QTLs, both of which have additive effects, indicates that the expression of these traits is also influenced by interactions between multiple genes. Our results provide additional genetic resources that can be used to precisely breed these traits in the future.

高油酸红花油因其氧化稳定性、营养价值和工业效益而成为重要的油料来源。鉴定与油质性状相关的分子标记有助于红花育种工作中的基因型选择。为了确定红花种子中籽油、油酸和亚油酸含量的遗传基础,研究人员从 Goldasht(低油酸品系)和 Mex 22-191(高油酸品系)杂交中培育了一个重组近交种群,每一代(从 F2 到 F9)都有单独的自花授粉植株。通过气相色谱法检测脂肪酸成分,然后进行 QTL 分析。结果表明脂肪酸成分的变异性很高,并产生了第一个高油酸红花基因型。利用 69 个 AFLP 和 45 个 ISSR 多态标记绘制了新的连接图,覆盖了红花基因组的 1472,441 cM。在 14 个基因组区域中,共检测到 63 个与油质有关的单个 QTL 和 238 个外显 QTL。在测定的性状中,发现了一些表型变异大于 10%的主要 QTL。这些结果表明,主要 QTL 在提高所用遗传物质的油酸含量方面可能起着重要作用。此外,较多的次要 QTL 和外显 QTL 都具有加性效应,这表明这些性状的表达还受到多个基因之间相互作用的影响。我们的研究结果提供了更多的遗传资源,可用于今后对这些性状进行精确育种。
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引用次数: 0
Exploring variability for morphological and quality traits in natural seedling origin mango germplasm of South Gujarat 探索南古吉拉特邦天然原种芒果种质的形态和品质特征变异性
IF 1.9 3区 农林科学 Q2 AGRONOMY Pub Date : 2024-09-10 DOI: 10.1007/s10681-024-03403-5
Nikita Patel, Y. N. Tandel, D. A. Chauhan, A. I. Patel

In order to determine the diversity in local seedling origin mango genotypes from different five districts (Navsari, Valsad, Dang, Tapi and Surat) of South Gujarat region during 2021–2023, which have been found in orchards or backyards by using IPGRI mango descriptor. The exploration of genetic resources was carried out to find alternative genotype against prevailing varieties in the state and it sustain mango production in future. A total of 113 mango seedlings were identified and characterized on basis of 7 qualitative, 12 quantitative and 6 biochemical parameters using Completely Randomized Design with three replications of quantitative characteristics. High variation among genotypes was observed with respect qualitative, quantitative and biochemical parameters. Ten superior genotypes were identified based on five commercially important traits viz., fruit weight (> 200 g), pulp percentage (> 60.00%), TSS (> 20 °Brix), shelf life (> 7 days) and overall acceptability (> 7 point). The genetic variability revealed that higher heritability coupled with higher genetic advance as per cent of mean for 12 quantitative characteristics namely mature fruit weight, fruit length, fruit width, pulp weight, peel weight, stone weight, TSS, acidity, ascorbic acid, total sugars, reducing sugars and non-reducing sugars. The First three Principal component contributed 70.21% of total variation and characters such as mature fruit weight, fruit length, fruit width, pulp weight, peel weight and stone weight most contributing towards diversity in germplasm. Hierarchical cluster analysis resulted the genotypes was grouped into three clusters and genotypes present in cluster III (20) and cluster I (39) had found most divers from each other.

为了确定 2021-2023 年期间南古吉拉特邦五个地区(纳夫萨里、瓦尔萨德、当、塔皮和苏拉特)当地芒果幼苗基因型的多样性,使用 IPGRI 芒果描述符在果园或后院发现了这些基因型。对遗传资源的发掘是为了找到替代该州现有品种的基因型,以维持未来的芒果生产。采用完全随机设计法,对 113 株芒果幼苗进行了鉴定,并根据 7 项定性参数、12 项定量参数和 6 项生化参数对其进行了定性,其中定量参数有三次重复。在定性、定量和生化参数方面,观察到不同基因型之间存在很大差异。根据果重(200 克)、果肉率(60.00%)、总糖度(20 °Brix)、货架期(7 天)和总体可接受性(7 分)这五个重要的商业性状,确定了 10 个优良基因型。遗传变异性表明,在成熟果重、果实长度、果实宽度、果肉重量、果皮重量、果核重量、总悬浮固体含量、酸度、抗坏血酸、总糖、还原糖和非还原糖这 12 个数量特征方面,遗传率较高,遗传进展占平均值的百分比也较高。前三个主成分占总变异的 70.21%,成熟果重、果实长度、果实宽度、果肉重量、果皮重量和果核重量等特征对种质多样性的贡献最大。分层聚类分析结果显示,基因型被分为三个群组,其中第 III 群组(20 个)和第 I 群组(39 个)中的基因型差异最大。
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引用次数: 0
Genome wide association mapping for cadmium tolerance and accumulation in an Aus population 澳大利亚人口镉耐受性和积累的全基因组关联图谱
IF 1.9 3区 农林科学 Q2 AGRONOMY Pub Date : 2024-09-09 DOI: 10.1007/s10681-024-03409-z
Ayotunde A. Adeosun, Adam H. Price, Gareth J. Norton

Rice consumption is a major exposure route of humans to cadmium, and cadmium also causes toxicity to rice plants. In this study the Bengal and Assam Aus Panel (BAAP) of rice was screened in hydroponics for cadmium tolerance and cadmium accumulation. Across the population, there were significant cultivar, treatment, and cultivar by treatment interactions for root and shoot length, and root, shoot and total dry weights. For treatment effects, the mean reductions caused by the cadmium treatment compared to control were 15%, 21%, 32%, 23% and 24% for root length, shoot length, root dry weight, shoot dry weight, and total dry weight respectively. Cultivars in the BAAP population displayed shoot cadmium concentrations in the range of 22–187 mg kg−1, with most of the rice cultivars having a cadmium concentration between 40 and 85 mg kg−1. GWA mapping identified 49 quantitative trait loci (QTL) across all traits, with 13 detected for more than one trait. Thirty-nine QTLs detected in this study were found to co-localise with previously identified QTLs for cadmium traits. A number of candidate genes for cadmium tolerance and accumulation were identified in these QTL regions. The QTL on chromosome 7 between 8.59 and 9.04 Mb contained both the candidate genes OsNRAMP1 and OsNRAMP5. The QTL on chromosome 6 at 29.20–29.73 Mb contained the candidate gene OsHMA2, while the QTL on chromosome 4 at 19.03 – 19.53 Mb contained the candidate gene OsHIPP29. The haplotype variation of these candidate genes is further explored in this study.

食用大米是人类接触镉的主要途径,镉也会对水稻植物产生毒性。本研究在水培法中对孟加拉和阿萨姆的水稻品种(BAAP)进行了耐镉和镉积累的筛选。在整个群体中,根长和芽长以及根重、芽重和总干重存在显著的栽培品种、处理和栽培品种与处理间的交互作用。在处理效应方面,与对照相比,镉处理导致的根长、芽长、根干重、芽干重和总干重的平均降幅分别为 15%、21%、32%、23% 和 24%。BAAP 群体中的栽培品种的嫩枝镉浓度在 22-187 毫克/千克之间,其中大多数水稻栽培品种的镉浓度在 40-85 毫克/千克之间。GWA 图谱在所有性状中发现了 49 个数量性状基因座(QTL),其中 13 个基因座检测到一个以上的性状。本研究中检测到的 39 个 QTL 与之前确定的镉性状 QTL 共同定位。在这些 QTL 区域中发现了一些镉耐受和积累的候选基因。第 7 号染色体上位于 8.59 和 9.04 Mb 之间的 QTL 包含候选基因 OsNRAMP1 和 OsNRAMP5。第 6 号染色体上位于 29.20-29.73 Mb 的 QTL 含有候选基因 OsHMA2,而第 4 号染色体上位于 19.03-19.53 Mb 的 QTL 含有候选基因 OsHIPP29。本研究将进一步探讨这些候选基因的单倍型变异。
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引用次数: 0
Policy dimension for promoting inter and intra-varietal diversity and evolutionary crop populations 促进品种间和品种内多样性及作物种群进化的政策层面
IF 1.9 3区 农林科学 Q2 AGRONOMY Pub Date : 2024-09-09 DOI: 10.1007/s10681-024-03405-3
Bal Krishna Joshi, Shree Prasad Neupane, Devendra Gauchan, Ajaya Karkee, Dipendra Kumar Ayer, Dejene Kassahun Mengistu

The value of broad genetic base cultivars is often underestimated in the formal seed system, which primarily emphasizes uniform, monogenotyped varieties to ensure food security. To gather insights on the significance of farmer’s varieties, cultivar mixtures, and evolutionary populations, a comprehensive approach involving surveys, focus group discussions, interviews, field observation and literature reviews was undertaken. Current legal frameworks in seed systems and variety handling predominantly serve the interests of seed companies, breeders, and extension officials, with limited consideration for the needs and preferences of farmers. This results in farmer’s varieties, characterized by their high genetic variation, as well as cultivar mixtures and evolutionary populations, receiving limited support within the policy framework. These broad genetic base cultivars have been cultivated and preserved by farmers for generations and exhibit resilience to diverse environmental conditions. The formal seed system, which has gained prominence, has separated farmers from a crucial aspect of their agricultural heritage. It is now managed by government offices and private seed companies, necessitating financial contributions from farmers to participate in the seed system. To encourage the cultivation of site-specific varieties with substantial genetic diversity, there is a need to promote these varieties, whether registered or unregistered, through a legal framework that encompasses all agricultural produces, not solely seeds. Such a framework acknowledges the capacity of farmers to independently maintain and cultivate their seeds, contributing to the preservation of genetic diversity and sustainable agriculture.

在正规种子系统中,广泛遗传基础的栽培品种的价值往往被低估,该系统主要强调统一、单一基因型的品种,以确保粮食安全。为了深入了解农民品种、混合栽培品种和进化种群的意义,我们采用了一种综合方法,包括调查、焦点小组讨论、访谈、实地观察和文献综述。目前种子系统和品种处理方面的法律框架主要服务于种子公司、育种者和推广官员的利益,对农民的需求和偏好考虑有限。这导致以遗传变异大为特点的农民品种以及混合栽培品种和进化种群在政策框架内得到的支持有限。这些遗传基础广泛的栽培品种经过农民世世代代的培育和保存,表现出对各种环境条件的适应能力。正规种子系统的地位日益突出,使农民与其农业遗产的一个重要方面分离开来。目前,该系统由政府部门和私营种子公司管理,农民必须出资才能参与种子系统。为了鼓励种植具有大量遗传多样性的特定地点品种,有必要通过一个涵盖所有农产品(而不仅仅是种子)的法律框架来推广这些品种,无论其是否注册。这种框架承认农民独立维护和培育种子的能力,有助于保护遗传多样性和可持续农业。
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引用次数: 0
Phenotypic diversity of key adaptive traits in advanced Nordic and Baltic spring wheat (Triticum aestivum L.) breeding material 北欧和波罗的海先进春小麦(Triticum aestivum L.)育种材料关键适应性状的表型多样性
IF 1.9 3区 农林科学 Q2 AGRONOMY Pub Date : 2024-09-06 DOI: 10.1007/s10681-024-03404-4
Anne Ingver, Andrii Gorash, Elena Ivandi, Vija Strazdina, Andrius Aleliūnas, Tanel Kaart, Valentina Fetere, Egon Meigas, Zaiga Jansone, Sahameh Shafiee, Tomasz Mroz, Mara Bleidere, Ebe Merilo, Morten Lillemo, Hannes Kollist, Gintaras Brazauskas, Ilmar Tamm

Wheat (Triticum aestivum L.) has become the most widely grown cereal crop in the Nordic-Baltic region, but due to climate change, its yields are under increasing risk. Here we present results of an international effort to use available wheat germplasm from the region to identify tools and genotypes for breeding wheat varieties with improved stability. We formed a panel of 300 spring wheat genotypes from the Nordic-Baltic region and studied their phenotypic diversity across environments to identify genotypes with high potential for adaptation to a changing climate. Field experiments were carried out in 2021 and 2022 in Estonia, Latvia, Lithuania and Norway. The performance and stability of yield (GY), protein content (PC), thousand kernel weight (TKW), test weight (TW), length of growing period (GP), and nine other traits were studied. Drought and excessive rainfall occurred in the Baltic countries in 2021–2022, whereas the weather in Norway was more stable. High variability for most traits, and significant GxE effects for all studied traits, were identified. We identified stable genotypes combining yield and quality using the AMMI model-based Weighted Average of Absolute Scores index (WAASB). Finally, we selected nineteen superior genotypes that combined high yield with high values of important quality traits. Thus, combining broad Nordic-Baltic wheat germplasm with extensive field phenotyping, we identified promising breeding material to develop climate-ready spring wheat varieties for the region.

小麦(Triticum aestivum L.)已成为北欧-波罗的海地区种植最广泛的谷类作物,但由于气候变化,其产量面临的风险越来越大。在此,我们介绍了一项国际性工作的成果,该工作旨在利用该地区现有的小麦种质,确定培育稳定性更强的小麦品种的工具和基因型。我们组建了一个由北欧-波罗的海地区 300 个春小麦基因型组成的小组,并研究了它们在不同环境下的表型多样性,以确定对气候变化具有高适应潜力的基因型。2021 年和 2022 年在爱沙尼亚、拉脱维亚、立陶宛和挪威进行了田间试验。对产量(GY)、蛋白质含量(PC)、千粒重(TKW)、测试重量(TW)、生长期长度(GP)和其他九个性状的表现和稳定性进行了研究。2021-2022年,波罗的海国家出现了干旱和过量降雨,而挪威的天气则较为稳定。大多数性状的变异性较高,所有研究性状的GxE效应显著。我们利用基于 AMMI 模型的加权平均绝对得分指数(WAASB)确定了兼具产量和品质的稳定基因型。最后,我们选出了 19 个兼具高产和重要品质性状高值的优良基因型。因此,结合广泛的北欧-波罗的海小麦种质和广泛的田间表型分析,我们确定了有前景的育种材料,为该地区开发气候适宜的春小麦品种。
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引用次数: 0
Comparing strategies for genomic predictions in interspecific biparental populations: a case study with the Rubus genus 种间双亲种群基因组预测策略比较:茜草属案例研究
IF 1.9 3区 农林科学 Q2 AGRONOMY Pub Date : 2024-09-04 DOI: 10.1007/s10681-024-03406-2
Allison Vieira da Silva, Melina Prado, Gabriela Romêro Campos, Karina Lima Reis Borges, Rafael Massahiro Yassue, Gustavo Husein, Marcel Bellato Sposito, Lilian Amorim, José Crossa, Roberto Fritsche-Neto

Genomic selection (GS) is becoming increasingly widespread and applied due to the promising results obtained, cost savings in generating single nucleotide polymorphism (SNP) markers, and the development of statistical models that allow to improve the analysis robustness and accuracy. The composition and size of the training population have a major influence on GS, which poses challenges for interspecific biparental populations. Another factor is the use of different reference genomes from other species to perform SNP calling, which could make it possible to explore variability in interspecific crosses comprehensively. Late leaf rust is a disease caused by the pathogen Acculeastrum americanum, and there are reports on genetic resistance in Rubus occidentalis, which leads to the need for interspecific hybridizations, aiming to combine the fruit quality of R. idaeus with the resistance of R. occidentalis. The present study was carried out with a population of 94 interspecific raspberry hybrids. We evaluated the effect of different reference genomes on the SNP markers discovery, as well as training population optimization strategies on the accuracy of genomic predictions, namely the CV-α, leaving-one-family-out (LOFO), pairwise families, and stratified k-fold. The average predictive accuracies ranged from − 0.33 to 0.44 and We demonstrated higher prediction accuracy and more precise estimates when we combined stratified sampling to compose the training set (CV-α and k-fold stratified CV) and the panel of Unique markers. These results corroborate that genomic prediction aligned with SNP calling and training population optimization strategies can significantly increase genetic gains in interspecific biparental crosses.

基因组选择(GS)的应用越来越广泛,这是因为它取得了可喜的成果,节省了生成单核苷酸多态性(SNP)标记的成本,而且统计模型的开发提高了分析的稳健性和准确性。训练群体的组成和规模对 GS 有重大影响,这对种间双亲群体构成了挑战。另一个因素是使用其他物种的不同参考基因组来进行 SNP 调用,这样可以全面探索种间杂交的变异性。晚叶锈病是由病原体 Acculeastrum americanum 引起的一种病害,有报道称西红宝石具有遗传抗性,因此需要进行种间杂交,目的是将西红宝石的果实品质与西红宝石的抗性结合起来。本研究使用了 94 个树莓种间杂交种。我们评估了不同参考基因组对 SNP 标记发现的影响,以及训练群体优化策略对基因组预测准确性的影响,即 CV-α、Leaving one-family-out (LOFO)、pairwise families 和 stratified k-fold。当我们结合分层抽样来组成训练集(CV-α 和 k-fold 分层 CV)和 Unique 标记小组时,我们证明了更高的预测准确率和更精确的估计值。这些结果证实,基因组预测与 SNP 调用和训练群体优化策略相结合,可以显著提高种间双亲杂交的遗传收益。
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引用次数: 0
WAASB-based stability analysis and simultaneous selection of forage sorghum for forage yield traits 基于 WAASB 的牧草高粱稳定性分析和牧草产量性状的同步选择
IF 1.9 3区 农林科学 Q2 AGRONOMY Pub Date : 2024-08-27 DOI: 10.1007/s10681-024-03397-0
Partha Pratim Behera, Avinash Singode, B. Venkatesh Bhat, Venkateswarlu Ronda, Nayanmoni Borah, Haiwang Yue, Harendra Verma, Jyoti Lekha Borah, Prasanta Kumar Majhi, Niharika Saharia, Labhya Rani Gogoi, Ramendra Nath Sarma

In response to the growing population and increasing demand for cattle products, enhancing sorghum forage yield is essential for ensuring food security. This study aimed to identify stable genotypes with high forage yields and key yield traits for sorghum breeding programs. Ninety-five forage sorghum lines were evaluated under five distinct climatic conditions over two years (2020–2021), revealing significant genotype × environment interaction (GEI) effects for 14 agronomic traits. Two BLUP-based mixed model stability methods, weight average absolute score based on BLUP (WAASB) and the multi-trait stability index (MTSI), were employed for stability analysis. Three genotypes, G90 (424B), G80 (382B) and G3 (349B) were identified stable and high yielding for forage yield based on WAASB based methods. The MTSI, a novel simultaneous selection index, effectively selected genotypes based on multiple agro-morphological traits, except for the leaf-to-stem ratio. Genotypes G81, G90, G80, and G89 were identified as desirable based on the MTSI. The strength and weakness plot is highlighted as a valuable graphical tool for identifying and selecting genotypes based on trait strengths and weaknesses. Among these, G90 (424B) and G80 (382B) stood out as superior, excelling in both forage yield and early maturity, as determined by WAASB based methods and MTSI method. These genotypes warrant further comprehensive investigation across diverse environments and show significant potential for future breeding programs.

为应对不断增长的人口和对牛产品日益增长的需求,提高高粱饲草产量对确保粮食安全至关重要。本研究旨在为高粱育种计划鉴定具有高饲草产量和关键产量性状的稳定基因型。研究人员对 95 个饲用高粱品系进行了为期两年(2020-2021 年)的评估,在五种不同的气候条件下,14 个农艺性状的基因型 × 环境互作(GEI)效应显著。稳定性分析采用了两种基于 BLUP 的混合模型稳定性方法,即基于 BLUP 的加权平均绝对得分法(WAASB)和多性状稳定性指数法(MTSI)。根据基于 WAASB 的方法,三个基因型 G90(424B)、G80(382B)和 G3(349B)被确定为饲料产量稳定的高产基因型。MTSI 是一种新型的同步选择指数,它能有效地根据多个农业形态性状(叶茎比除外)选择基因型。根据 MTSI,基因型 G81、G90、G80 和 G89 被确定为理想基因型。优缺点图是根据性状优缺点识别和选择基因型的重要图形工具。在这些基因型中,G90(424B)和 G80(382B)表现突出,根据基于 WAASB 的方法和 MTSI 方法测定,它们在牧草产量和早熟性方面都很优秀。这些基因型值得在不同环境下进行进一步的综合研究,并显示出未来育种计划的巨大潜力。
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引用次数: 0
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Euphytica
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