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[学术文献 ] Insights Into the Genetics of the Zhonghua 11 Resistance to Meloidogyne graminicola and Its Molecular Determinism in Rice 进入全文
FRONTIERS IN PLANT SCIENCE
Meloidogyne graminicola is a widely spread nematode pest of rice that reduces crop yield up to 20% on average in Asia, with devastating consequences for local and global rice production. Due to the ban on many chemical nematicides and the recent changes in water management practices in rice agriculture, an even greater impact of M. graminicola can be expected in the future, stressing the demand for the development of new sustainable nematode management solutions. Recently, a source of resistance to M. graminicola was identified in the Oryza sativa japonica rice variety Zhonghua 11 (Zh11). In the present study, we examine the genetics of the Zh11 resistance to M. graminicola and provide new insights into its cellular and molecular mechanisms. The segregation of the resistance in F-2 hybrid populations indicated that two dominant genes may be contributing to the resistance. The incompatible interaction of M. graminicola in Zh11 was distinguished by a lack of swelling of the root tips normally observed in compatible interactions. At the cellular level, the incompatible interaction was characterised by a rapid accumulation of reactive oxygen species in the vicinity of the nematodes, accompanied by extensive necrosis of neighbouring cells. The expression profiles of several genes involved in plant immunity were analysed at the early stages of infection during compatible (susceptible plant) and incompatible (resistant plant) interactions. Notably, the expression of OsAtg4 and OsAtg7, significantly increased in roots of resistant plants in parallel with the cell death response, suggesting that autophagy is activated and may contribute to the resistance-mediated hypersensitive response. Similarly, transcriptional regulation of genes involved in hormonal pathways in Zh11 indicated that salicylate signalling may be important in the resistance response towards M. graminicola. Finally, the nature of the resistance to M. graminicola and the potential exploitation of the Zh11 resistance for breeding are discussed.
[学术文献 ] Grain yield performance of hybrid rice in relation to inbred cultivars in long-term multi-environment tests in India 进入全文
CROP SCIENCE
We analyzed the yield data of 2,070 rice hybrid F-1 genotypes with inbred local cultivars (ILCv) evaluated over 32 yr (from 1988 to 2019) in 2,376 multi-environment experiments executed at 102 locations in the irrigated ecosystem across India. The genetic gain or loss in yield of hybrid F-1 genotypes estimated over the test duration was nonsignificant. The differences were highly significant between the means of group of F-1 hybrid genotypes with yields higher than ILCvs in 985 experiments and the group of F-1 hybrid genotypes with yields lower than ILCvs in 962 experiments. Hybrids produced 10% more yield (728-2,588 kg ha(-1)) than ILCvs in 672 experiments at several locations. Our analyses have established that grain yields of 7.0-7.9 Mg ha(-1), were harvested in hybrid F-1 genotypes with early- (110-120 d), mid-early- (121-130 d), and medium- (131-140 d) maturity duration, and in those with medium slender grains (130 +/- 5 d) at many locations in 374 out of the 985 experiments. A higher level of rice (Oryza sativa L.) productivity per day (62-63 kg ha(-1)) was recorded with the early-maturing and mid-early-maturing hybrid genotypes. Both the hybrid F-1 genotypes and ILCvs produced grain yields (>= 10 Mg ha(-1)) similar to values that were recorded previously with commercial inbred cultivars since 1968 at many locations. The attainable grain yield records of ILCvs were not broken by the yields of hybrid F-1 genotypes. Hence the doubt arises whether there was any overestimation of hybrid genotypes or an underestimation of inbred yields. Therefore, any genetic gain or loss for grain yields in new genotypes developed in experiments can be estimated only when ILCvs produce their attainable yield recorded previously. There is scope for breeders to limit test locations to represent specific target areas to avoid data loss.
[学术文献 ] Uncovering the Novel QTLs and Candidate Genes of Salt Tolerance in Rice with Linkage Mapping, RTM-GWAS, and RNA-seq 进入全文
RICE
Salinity is a major abiotic stress that limits plant growth and crop productivity. Indica rice and japonica rice show significant differences in tolerance to abiotic stress, and it is considered a feasible method to breed progeny with stronger tolerance to abiotic stress by crossing indica and japonica rice. We herein developed a high-generation recombinant inbred lines (RILs) from Luohui 9 (indica) X RPY geng (japonica). Based on the high-density bin map of this RILs population, salt tolerance QTLs controlling final survival rates were analyzed by linkage mapping and RTM-GWAS methods. A total of seven QTLs were identified on chromosome 3, 4, 5, 6, and 8. qST-3.1, qST-5.1, qST-6.1, and qST-6.2 were novel salt tolerance QTLs in this study and their function were functionally verified by comparative analysis of parental genotype RILs. The gene aggregation result of these four new QTLs emphasized that the combination of the four QTL synergistic genotypes can significantly improve the salt stress tolerance of rice. By comparing the transcriptomes of the root tissues of the parents' seedlings, at 3 days and 7 days after salt treatment, we then achieved fine mapping of QTLs based on differentially expressed genes (DEGs) identification and DEGs annotations, namely, LOC_Os06g01250 in qST-6.1, LOC_Os06g37300 in qST-6.2, LOC_Os05g14880 in qST-5.1. The homologous genes of these candidate genes were involved in abiotic stress tolerance in different plants. These results indicated that LOC_Os05g14880, LOC_Os06g01250, and LOC_Os06g37300 were the candidate genes of qST-5.1, qST-6.1, and qST-6.2. Our finding provided novel salt tolerance-related QTLs, candidate genes, and several RILs with better tolerance, which will facilitate breeding for improved salt tolerance of rice varieties and promote the exploration tolerance mechanisms of rice salt stress.
[前沿资讯 ] 科学家解码东北水稻育种史 进入全文
中国科学院
随着功能基因组研究的深入和现代分子生物学技术的发展，作物育种正由传统的“经验育种”“标记辅助育种”阶段向高效精准的“全基因组设计育种”阶段过渡。目前，对全基因组设计育种技术体系的进一步完善是作物遗传育种领域的研究热点。由于品种选育固有的地域特性及年代特性，设计育种的成功实施依赖于对基因功能或基因组的深入注释，也在很大程度上有赖于人们对过去经验育种历史经纬的充分认知。然而，长期以来，从全基因组视角系统诠释特定区域经验育种规律始终颇具挑战性。2月9日，中国科学院遗传与发育生物学研究所储成才团队、李家洋院士团队，联合东北地理与农业生态研究所卜庆云团队等，在National Science Review上，发表了题为Genomic Decoding of Breeding History to Guide Breeding-by-Design in Rice的研究论文，构建了我国东北稻区经验育种史的分子诠释模型，归纳并验证了该地区不同时期水稻育种规律与未来趋势。水稻作为南方温热地区起源的作物，在高纬度地区的栽培历史较短。其中，我国东北是全球稻米种植区域中纬度最高的地区之一（图1）。得益于育种家长期对水稻抽穗期、耐冷性、抗病性、食味品质、抗倒伏性等关键性状的选择和改良，使其能够适应高纬度环境并借助独特的生态环境产出最为优质的大米。当前，东北稻区已成为国内最重要的优质稻米产区。东北地区水稻栽培及育种史相对简明且可追溯，使得从全基因组层面解码经验育种规律、建立基础诠释模型，并为全基因组设计育种提供范本成为可能。同时，该稻区在我国优质稻米供应上占据的重要地位，也使得相关研究在保障我国优质稻米生产方面具有重要的实践意义和紧迫性。为全面阐释东北地区品种性状演变趋势以及基因型组合和利用情况，研究团队收集了涵盖东北稻区自1940年代到2010年代选育或引种的546份水稻品种资源，并进行重测序，同时，对22个农艺性状表型进行调查和全基因组关联分析。研究发现，不同地理来源品种表现出显著的农艺性状差异，反映其环境适应需要和品种特性偏好。生育期、低温结实率、稻瘟病抗性和粒型上表现出显著的年代差异，意味着栽培技术和市场需求变化影响育种家对产量、抗性、品质的选择。也就是说，不同育种家对育种的领悟、偏好及经验等在整体上具有区域以及年代特征，这些特征最终体现在品种表型所对应的基因型上。全基因组SNP标记的群体结构分析揭示，东北地区水稻品种可归类到3个具有不同进化特征的亚群（图2），以石狩白毛为骨干的K3G1亚群在20世纪80年代前的黑龙江品种中占主导地位，随后被以虾夷和空育131为骨干的K3G2亚群取代；而以富士光和藤系138为骨干的K3G3亚群主要分布在辽宁和吉林，但随着时间推移，其在黑龙江省的占比越来越高。遗传背景狭窄是温带粳稻育种的重要限制因素。我国东北地区的育种家很早提出并引入籼稻遗传成分对粳稻品种进行改良。研究采用群体结构分析、遗传渗入分析、全基因组关联分析和染色体片段代换系等技术手段，确认了籼稻渗入对东北水稻育种的重要贡献，特别是对稻瘟病抗性等位基因（如Pi-ta、Ptr）的引入以及穗产量性状（qSB2、qSB8、qSB10、qPL9等）改良的重要作用。进一步通过将品种选育印记追溯到123个已知或新检测到的QTL位点以及大量籼稻渗入片段，研究总结了一些具有年代特征的关键性QTL位点或渗入片段，为后继的品种设计选育提供了依据（图2）。2009年，李家洋率领的育种团队，对东北水稻品种的现状与需求开展了深入的实地考察与系统分析，在此基础上建立了分子设计育种体系，快速培育了高产、高抗、优质的“中科发”系列水稻品种。其中，代表性品种“中科发5号”于2018年通过国家审定，随后在东北大面积推广，迅速成为黑龙江省与吉林省的主载品种。本研究解析中科发5号发现，其优异等位基因组合与上述分析所揭示的东北地区品种选育趋势高度契合，是上述全基因组诠释分析的最佳例证。中科发5号通过将富含籼稻渗入片段的南方优质粳稻品种长粒粳、东北地区骨干稳产品种空育131以及K3G3亚群的吉粳88进行组配，整合了抽穗期决定基因Hd1，稻瘟病抗性位点Pita、Ptr、Pib，抗倒伏位点SCM2，粒型位点GW5、GS3、GL7，穗产量性状位点qSB2、qSB8、qSB10等一系列分子模块，在高纬度稻区实现了丰产、优质、抗病、抗倒伏等优异性状聚合，取得了东北水稻育种和生产推广上的成功。该成果全面解析了中国东北地区水稻遗传结构和育种关键位点，揭示了经验育种反馈在基因组上的普遍规律，为东北水稻品种的全基因组设计育种提供参考依据和范例，有望进一步推动水稻分子设计育种的完善和实施，并为其他作物经验育种史的解析和分子设计育种研究提供参考。研究工作得到中科院战略性先导科技专项、国家重点研发计划和国家自然科学基金的支持。
[前沿资讯 ] 科研人员综述智能时代粮食作物中镉污染风险评估和控制策略 进入全文
中科院植物所
镉是环境中广泛存在的有毒重金属元素，可随食物链累积到人体，世界各国都极其重视镉的健康风险。减少粮食作物中籽粒镉含量的策略可从根本上降低民众镉暴露的风险，是保障国家粮食安全和国民健康的重要举措。大数据和人工智能的发展有效促进了环境科学、生命科学和信息科学的融合，为高效、稳定、精准化评估和控制粮食作物中的镉污染风险带来了新机遇。中科院植物所何振艳团队长期从事低积累重金属作物创制和重金属污染农田安全利用研究，近年来在作物镉污染评估与预警、作物镉积累特性及其分子调控网络解析、低镉作物全基因组选择育种和和材料创制等方面取得了系列进展。近期，该团队发表了粮食作物中镉污染风险评估和控制策略的综述文章。研究提出了控制粮食作物中镉污染风险的“基因型”和“环境型”双引擎驱动的智能化策略。从基因型角度，策略是定向培育和智能创制低镉作物新型种质。科研人员对三大主粮作物的籽粒镉超标情况进行荟萃分析，发现低、中、高镉污染的田间试验均有作物籽粒镉积累超标现象，且物种间的镉污染风险差异显著；探讨了“优异变异”在未来低镉作物新型种质创制中的重要性，并结合大数据智能化技术提出两种范式：一是通过连锁关联定位、全基因组关联研究和全基因组选择等手段挖掘和聚合自然种群中的优异变异，精准定向培育低镉作物，二是利用同源建模、蛋白从头设计、基因编辑等手段设计和实施自然种群中不存在的人工优异变异，创制低镉作物新种质。从环境型角度，策略是构建土壤环境镉阈值-不同粮食作物品种-籽粒镉含量的智能化模型，明确不同土壤的适种品种。通过分析影响作物镉积累的土壤环境因素，讨论了基于线性回归、机器学习等算法构建的环境型-表型模型预测作物适种土壤环境镉阈值的重要性，展望了智能农业、物联网等技术在精准控制土壤环境镉阈值中的应用潜力。研究期冀在环境科学、生物科学、大数据、人工智能等多学科、多技术的支持下，作物镉污染风险控制朝着智能化、高效化、定向化方向发展，最终实现从“经验”到“智能”的革命性转变，推动农业绿色可持续发展。
[前沿资讯 ] 研究发现野生稻基因参与新的水稻粒长调控途径 进入全文
中国农业科学院作物科学研究所
1月20日,中国农业科学院作物科学研究所水稻优异种质资源发掘与创新利用创新团队研究发现了一个来自野生稻的新的基因位点，可以提高栽培稻粒长和粒重，揭示了新的水稻粒长调控途径，为水稻育种提供了理论基础和新的基因资源。相关研究结果在线发表在《植物生物技术（Plant Biotechnology Journal）》上。野生稻中丰富的等位变异一直是栽培稻育种的基因库。在漫长的驯化过程中，大量影响产量的优异基因位点被人工选择聚合在栽培稻中，因此绝大多数栽培稻种质资源的种子，都比野生稻的种子大的多。虽然野生稻的产量性状远劣于栽培稻，仍有研究报道在野生稻中存在可提高产量的数量性状基因座。但是，一直未有野生稻正调控粒长基因的报道。该团队历时十余年，构建了一套以栽培稻9311为受体亲本，覆盖野生稻基因组的染色体片段置换系，经过多年表型鉴定，精细定位到一个与粒长相关的基因位点。试验表明，野生稻GL12w的近等基因系和转基因过表达株系的粒长、粒重均有提高，且粒长和粒重的增加呈正相关；而敲除该基因后粒长、粒重恢复至亲本水平。序列分析发现，GL12w存在3个基因突变的功能位点。研究还发现，该基因在籼稻群体中仅有少量的野生稻基因型，平均粒长显著增加。进一步的机理研究表明，GL12w提高颖壳细胞的长度以及授粉后的灌浆速度，影响了水稻粒长相关基因的转录水平，可直接靶向激活生长调节因子GS2的转录。研究人员将近等基因系与9311分别作为恢复系创制了两份杂交种，前者作为恢复系的杂交种粒长粒重显著提高，证实了GL12w在不同的栽培稻遗传背景下具有提高粒长粒重的效应。本研究为野生稻资源的创新利用，以及水稻粒长相关调控途径的研究提供了新的思路。
