是金子无论在何处都发光: 玉米和水稻驯化中的趋同选择

野生植物的驯化为人类定居与文明起源奠定了重要基础。在世界范围内不同地区生活的古人类分别对当地不同的野生植物进行了驯化, 而经过驯化的作物常常表现出相似的驯化综合性状。在基因组层面上对趋同选择规律的解析, 可为作物育种提供重要信息与遗传资源。近日, 中国农业大学杨小红/李建生和华中农业大学严建兵领衔的团队从单基因和全基因组2个层次系统解析了玉米(Zea mays)和水稻(Oryza sativa)趋同选择的遗传基础, 发现玉米KRN2与水稻OsKRN2受到了趋同选择, 并通过相似的途径调控玉米与水稻的粒数与产量。他们还发现玉米与水稻在全基因组范围内存在大量趋同选择同源基因对(gene pair), 这些基因在淀粉代谢、糖及辅酶合成等途径特异富集。该研究不仅克隆了在玉米与水稻中均具有重要育种价值的趋同选择同源基因对KRN2/OsKRN2, 而且在全基因组水平上揭示了玉米与水稻趋同选择的规律, 为进一步解析驯化综合性状形成的分子机理及其在育种中的应用奠定了重要理论基础。     

从头驯化：作物品种设计与培育的新方向

全球气候变化对农业生产带来了巨大挑战。在农业投入减少的前提下如何保障粮食生产持续稳步增长,满足人们吃饱、吃好的需求是亟需考虑的问题。培育高产、稳产、绿色、营养的新型作物品种仍然是解决该挑战的有效措施之一。作物新品种的培育高度依赖育种材料遗传多样性的拓宽和育种技术的创新。从头驯化是一种作物品种创新的全新育种策略,以具有某些优异性状的未驯化、半驯化植物作为底盘物种,通过农艺性状重新设计和驯化基因导入实现野生植物快速驯化,从而满足人类多样化需求。本文回顾了作物驯化、遗传改良历程,阐明了丰富作物多样性的必要性,强调野生植物丰富的遗传多样性对于拓展作物重新设计空间的重要价值,提出育种策略革新是加速作物育种的关键,探讨了通过从头驯化快速培育新型作物品种的可行性和发展前景。     

2012年第11期《遗传》封面说明

作物的驯化是人类从开始种植和储存的野生作物中选择优良性状,使之形态特征适应于农业生产方向进化的过程,因此,大部分种子作物驯化后在落粒性、种子休眠和植株形态等方面都出现了相似的变化。水稻是研究谷类作物驯化的良好模式生物。稻属包含2种栽培稻,分别为亚洲栽培稻(Oryza sativa L.)和非洲栽培稻(O. glaberrima Steud.),其中亚洲栽培稻遍布全世界,包含两个主要亚种,粳稻亚种(O. sativa L. ssp. japonica)和籼稻亚种(O. sativa L. ssp. indica)。稻属丰富的近缘种和广泛的地域分布非常有利于研究确定现代栽培稻的驯化地域。此外,水稻基因组较小、具高质量精细图谱,加上功能基因研究上的进展,也为深入开展水稻驯化进程研究奠定了基础。详见本期第XX-XX页区树俊,汪鸿儒,储成才“亚洲栽培稻主要驯化性状研究进展”,对水稻关键驯化性状研究进行的比较全面的综述。封面图中央是选取23株AA基因组的亚洲栽培稻及其近缘野生稻,利用水稻驯化过程中受到选择的控制稻壳颜色基因Bh4上下游各50 kb中的SNP位点所构建的进化树;图外从左下至右下沿顺时针方向,反映的是水稻驯化过程中稻壳颜色、谷粒形状、穗型的变化趋势。 区树俊,汪鸿儒,储成才（绘图：区树俊）     

主要农作物驯化研究进展与展望

农作物的驯化过程与农耕文明的发端密切相关,是作物种质资源遗传基础不断丰富衍化,利用价值不断完善的主要途径之一。本文重点从作物驯化的主要性状、基因组遗传区段、重要驯化基因的克隆、作物驯化后的传播与基因渗透、作物驯化理论与研究方法以及作物驯化研究的新趋势等方面评述近年来取得的主要研究进展,讨论研究存在的主要问题并对深入开展作物驯化研究进行展望。     

作物驯化的遗传学研究及其在大豆育种中的应用

驯化遗传学是进化生物学研究的一个重要分支, 对作物驯化历程进行深入探索, 可以更好地认识人类早期农耕文明的产生和发展, 了解物种的形成乃至生命的起源和进化, 对指导人们利用野生资源来改良现有的栽培作物和培育新的有价值的品种也具有重要的意义。本文综述了作物驯化的遗传学研究内容和进展, 以及重要作物大豆驯化起源的研究概况, 探讨了目前作物驯化研究对大豆驯化遗传学及野生大豆资源综合利用的指导意义。     

作物驯化的遗传学研究及其在大豆育种中的应用

驯化遗传学是进化生物学研究的一个重要分支,对作物驯化历程进行深入探索,可以更好地认识人类早期农耕文明的产生和发展,了解物种的形成乃至生命的起源和进化,对指导人们利用野生资源来改良现有的栽培作物和培育新的有价值的品种也具有重要的意义。本文综述了作物驯化的遗传学研究内容和进展,以及重要作物大豆驯化起源的研究概况,探讨了目前作物驯化研究对大豆驯化遗传学及野生大豆资源综合利用的指导意义。     

NGS技术在作物基因组研究中的应用

新一代测序技术(Next-generation sequencing,NGS)在阐明复杂和高度重复的基因组结构,DNA序列与基因组结构变异同重要农艺性状之间的关系等方面具有重要作用。从NGS系统的开发与作物基因组测序,NGS与转录组分析,NGS与全基因组关联图谱,及SNPs开发与预测育种等方面,综述了NGS技术在作物基因组研究中的应用,可为作物基因组研究提供理论基础。     

重新设计与快速驯化创造新型作物

作物驯化和遗传改良对于产量性状的过分追求常导致其抗逆性和遗传多样性的降低,在全球气候变化加剧和自然灾害频发的大背景下,该效应使得世界粮食稳产和食物安全面临威胁,亟需创新育种策略。作物重新设计与快速驯化是指选用耐逆、品质营养等性状或其他目标性状优异的野生或者半野生植物,综合运用基因组学、基因编辑和合成生物学等方法,对其农艺性状进行重新设计,在保持其原有优异性状的前提下,快速驯化获得新型作物的全新育种策略。本文回顾了作物驯化的发展历程及其对农业发展和人类文明的贡献,着重阐述了育种策略创新的紧迫性,并对作物重新设计与快速驯化创造新型作物的可行性、最新进展和发展前景进行探讨和展望。     

人类基因组的研究进展

人类基因组的研究进展达来内蒙古大学生物学系,呼和浩特,０１００２１）人类基因组计划是１９９０年１０月正式实施的为期１５年耗资３０亿美元的宏伟工程。它的任务是完成高精度的人类基因组遗传学图谱和物理图谱,测定人和几个模式生物的基因组ＤＮＡ序列,是广泛的国...     

SNP标记与大豆基因组作图

大豆是重要的粮油作物,在农业和经济中具有重要地位,因此对大豆基因的研究具有重要的意义。利用分子标记构建的遗传图谱是植物基因组结构和功能分析的有力工具。本文综述了SNP标记在大豆基因组中的开发、大豆基因组作图的研究概况及SNP标记在其中的应用。     

2021年中国植物科学重要研究进展

2021年中国植物科学家在国际综合性学术期刊及植物科学主流期刊发表的论文数量相比2020年显著增加, 在雌雄细胞识别与受精、干细胞命运决定、菌根共生、光合膜蛋白复合体、氮磷养分利用、先天免疫、作物从头驯化与基因组设计等方面取得了重要研究进展,“异源四倍体野生稻快速从头驯化”入选2021年度“中国生命科学十大进展”。该文总结了2021年度我国植物科学研究取得的成绩, 简要介绍了30项重要进展, 以帮助读者了解我国植物科学的发展态势, 思考如何更好地将植物科学研究与国家重大需求有效衔接。     

水稻产量相关性状驯化研究进展

水稻具有悠久的栽培历史,是重要的粮食作物,养育了1/3的世界人口。现代栽培稻(Oryza sativa)由野生稻(O.rufipogon)驯化而来,产量是驯化筛选的关键性状之一。株型、穗型和种子大小是决定水稻产量的重要性状,这些性状在水稻栽培过程中均受到了定向筛选。该文以水稻产量性状为核心,综述了株型、穗型和种子大小等性状的驯化分子机理研究进展,讨论了水稻产量驯化研究中存在的问题,展望了驯化性状和相关基因的研究前景,以期为水稻产量相关性状的驯化机理研究和水稻育种工作提供有价值的线索。     

Characterization of pre-insertion loci of de novo L1 insertions

The human Long Interspersed Element-1 (LINE-1) and the Short Interspersed Element (SINE) Alu comprise 28% of the human genome. They share the same L1-encoded endonuclease for insertion, which recognizes an A+T-rich sequence. Under a simple model of insertion distribution, this nucleotide preference would lead to the prediction that the populations of both elements would be biased towards A+T-rich regions. Genomic L1 elements do show an A+T-rich bias. In contrast, Alu is biased towards G+C-rich regions when compared to the genome average. Several analyses have demonstrated that relatively recent insertions of both elements show less G+C content bias relative to older elements. We have analyzed the repetitive element and G+C composition of more than 100 pre-insertion loci derived from de novo L1 insertions in cultured human cancer cells, which should represent an evolutionarily unbiased set of insertions. An A+T-rich bias is observed in the 50 bp flanking the endonuclease target site, consistent with the known target site for the L1 endonuclease. The L1, Alu, and G+C content of 20 kb of the de novo pre-insertion loci shows a different set of biases than that observed for fixed L1s in the human genome. In contrast to the insertion sites of genomic L1s, the de novo L1 pre-insertion loci are relatively L1-poor, Alu-rich and G+C neutral. Finally, a statistically significant cluster of de novo L1 insertions was localized in the vicinity of the c-myc gene. These results suggest that the initial insertion preference of L1, while A+T-rich in the initial vicinity of the break site, can be influenced by the broader content of the flanking genomic region and have implications for understanding the dynamics of L1 and Alu distributions in the human genome.     

Application and future perspective of CRISPR/Cas9 genome editing in fruit crops

Fruit crops, including apple, orange, grape,banana, strawberry, watermelon, kiwifruit and tomato, not only provide essential nutrients for human life but also contribute to the major agricultural output and economic growth of many countries and regions in the world. Recent advancements in genome editing provides an unprecedented opportunity for the genetic improvement of these agronomically important fruit crops. Here, we summarize recent reports of applying CRISPR/Cas9 to fruit crops,including efforts to reduce disease susceptibility, change plant architecture or flower morphology, improve fruit quality traits, and increase fruit yield. We discuss challenges facing fruit crops as well as new improvements and platforms that could be used to facilitate genome editing in fruit crops, including d Cas9-base-editing to introduce desirable alleles and heat treatment to increase editing efficiency. In addition, we highlight what we see as potentially revolutionary development ranging from transgene-free genome editing to de novo domestication of wild relatives. Without doubt, we now see only the beginning of what will eventually be possible with the use of the CRISPR/Cas9 toolkit. Efforts to communicate with the public and an emphasis on the manipulation of consumerfriendly traits will be critical to facilitate public acceptance of genetically engineered fruits with this new technology.     

Mutation as an origin of genetic variability in Helicobacter pylori

The availability of two complete Helicobacter pylori genome sequences and recent studies of its population genetics have provided a detailed picture of genetic diversity in this important human gastric pathogen. It is believed that, in addition to genetic recombination, de novo mutation could have a role in generating the high level of genetic variation in H. pylori.     

High efficient multisites genome editing in allotetraploid cotton (Gossypium hirsutum) using CRISPR/Cas9 system

Gossypium hirsutum is an allotetraploid with a complex genome. Most genes have multiple copies that belong to At and Dt subgenomes. Sequence similarity is also very high between gene homologues. To efficiently achieve site/gene‐specific mutation is quite needed. Due to its high efficiency and robustness, the CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 system has exerted broad site‐specific genome editing from prokaryotes to eukaryotes. In this study, we utilized a CRISPR/Cas9 system to generate two sgRNAs in a single vector to conduct multiple sites genome editing in allotetraploid cotton. An exogenously transformed gene Discosoma red fluorescent protein2(DsRed2) and an endogenous gene GhCLA1 were chosen as targets. The DsRed2‐edited plants in T0 generation reverted its traits to wild type, with vanished red fluorescence the whole plants. Besides, the mutated phenotype and genotype were inherited to their T1 progenies. For the endogenous gene GhCLA1, 75% of regenerated plants exhibited albino phenotype with obvious nucleotides and DNA fragments deletion. The efficiency of gene editing at each target site is 66.7–100%. The mutation genotype was checked for both genes with Sanger sequencing. Barcode‐based high‐throughput sequencing, which could be highly efficient for genotyping to a population of mutants, was conducted in GhCLA1‐edited T0 plants and it matched well with Sanger sequencing results. No off‐target editing was detected at the potential off‐target sites. These results prove that the CRISPR/Cas9 system is highly efficient and reliable for allotetraploid cotton genome editing.     

Genomic landscape of parallel domestication of upland rice and its implications

Parallel domestication has been widely acknowledged but itsgenetic basis remains largely unclear. As an important rice ecotype, upland rice was assumedly domesticated multiple times in two rice subspecies (Indica and Japonica) and provides a feasible system to explore the genetic basis of parallel domestication. To uncover the genome‐wide pattern of genetic differentiation between upland and lowland rice and explore the parallelism of genetic changes during upland rice domestication, we obtained whole‐genome sequences of 95 rice landraces and yielded genome‐wide expression data for five tissues of representative accessions of upland and lowland rice. Our phylogenetic analyses confirmed multiple domestications of the upland ecotype in two rice subspecies. Genomic scans based on resequencing data identified substantial differentiation between the upland and lowland ecotypes with 11.4% and 14.8% of the genome diverged between the two ecotypes in Indica and Japonica, respectively. Further genome‐wide gene expression analyses found that 30% of effectively expressed genes were significantly differentiated between two ecotypes, indicating the importance of regulation changes in the domestication of upland rice. Importantly, we found that only 1.8% of differentiated genomes and 1.6% of differentially expressed genes were shared by upland Indica and upland Japonica, suggestive of largely unparallel genetic alterations during upland rice domestication. These findings not only provide new insights into the genetic basis of parallel domestication at the genome scale but could also facilitate geneticimprovement and breeding of rice and crops in general.