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）     

奶牛重要经济性状全基因组关联分析研究进展

产奶性状是奶牛最重要的生产性状,随着平衡育种理念的提出和发展,繁殖性状、体型性状、健康性状和长寿性等功能性状也逐渐被重视并纳入育种规划中。鉴定产奶性状和功能性状主效基因或遗传标记并将之应用于奶牛标记辅助选择可望加快遗传进展。随着高密度SNP标记的高通量检测技术的发展,全基因组关联分析已成为鉴定畜禽重要经济性状基因的重要途径。文章对奶牛产奶性状和功能性状全基因组关联分析研究进展进行综述。     

亚洲栽培稻起源和驯化研究新进展

近日,中国科学院古脊椎动物与古人类研究所同高能物理研究所合作,利用高清晰度工业CT对柳江头骨化石进行了扫描和三维重建,这是我国学者首次利用CT技术清晰展示的古人类脑的形态特征。20世纪50年代发现于广西柳江的人类头骨化石,是迄今在华南地区发现的保存最为完整的更新世晚期人类化石,其与北京周口店及其他古人类化石以及现代人颅内模比较,     

中国多孔菌驯化栽培研究进展

总结和概述了2018—2022年间我国真菌学者对多孔菌驯化栽培研究的进展,期间我国对20种多孔菌进行了生物学研究,并在此基础上驯化栽培、成功发育成子实体,为我国药用真菌产业发展提供了重要资源基础和技术支撑。     

奶牛重要经济性状全基因组关联分析研究进展

产奶性状是奶牛最重要的生产性状, 随着平衡育种理念的提出和发展, 繁殖性状、体型性状、健康性状和长寿性等功能性状也逐渐被重视并纳入育种规划中。鉴定产奶性状和功能性状主效基因或遗传标记并将之应用于奶牛标记辅助选择可望加快遗传进展。随着高密度SNP标记的高通量检测技术的发展, 全基因组关联分析已成为鉴定畜禽重要经济性状基因的重要途径。文章对奶牛产奶性状和功能性状全基因组关联分析研究进展进行综述。     

基于SSR标记初步定位小豆驯化相关性状QTL

炸荚和籽粒硬实性是野生小豆的主要特性,严重制约着野生小豆资源的利用,解析这些性状的遗传机理,对培育优良小豆新品种具有重要意义。本研究基于中红5号和野生小豆(Vigna angularis var.n ipponensis)杂交衍生的重组自交系,开展炸荚和籽粒硬实等驯化相关性状鉴定及SSR标记分析。表型分析显示荚皮卷曲数、炸荚率及籽粒硬实率均不符合典型正态分布。构建了包含111个SSR标记、11个连锁群的小豆遗传连锁图谱,总长3813.5 cM,标记间平均距离为34.35 cM。连锁分析共发掘到与2021年炸荚率和荚皮卷曲数相关QTL 19个,与2022年炸荚率及荚皮卷曲数相关QTL 13个,其中不同年份重复检测到的荚皮卷曲数相关QTL 2个,重复检测到的炸荚率相关QTL 3个。籽粒硬实相关QTL 4个,其中位于LG11的QTL分别与炸荚率及2022年荚皮卷曲数相关QTL重叠。本研究结果为进一步开展小豆驯化相关基因的精细定位及机理解析奠定了基础。     

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。     

《植物细胞》：研究证实栽培稻芒缺失受人工驯化选择

中科院上海生科院植物生理生态所、国家基因研究中心韩斌团队,通过图位克隆法克隆了野生稻控制芒发育的An-1基因。该基因编码一个bHLH转录调控因子。从而揭开了相关水稻遗传之谜。相关成果日前在线发表于《植物细胞》杂志。     

青藏高原老芒麦落粒动态与农艺性状及地理分布关系研究

该试验以6份来自青藏高原东北缘老芒麦为研究材料,利用断裂拉伸张力(BTS)法评价其不同发育时期落粒率,并分析落粒率与其他农艺性状和地理信息的相关性,为老芒麦种子生产及低落粒种质筛选提供参考。结果表明:(1)老芒麦种子落粒率在抽穗后1周和2周较低,而在抽穗后3周与4周有所升高,在抽穗后5周种子落粒率最高(BTS=0.52N);供试材料ZHN03在测定时期内种子落粒率均低于其他材料,而材料XH09在抽穗后5周种子落粒率最高(BTS=0.33N)。(2)在种子脱落期间,低落粒与高落粒老芒麦的6个农艺性状变化趋势相似;老芒麦落粒性与5个农艺性状有密切关联,其中BTS值与穗长、小穗数和小穗小花数呈显著正相关关系,与芒长和千粒重具有极显著正相关关系。(3)老芒麦穗长与纬度间具有极显著负相关关系,芒长与纬度间具有显著负相关关系;千粒重与经度间具有极显著负相关关系,与海拔间具有极显著正相关关系;BTS值与小穗数呈显著正相关关系,与芒长和小穗小花数呈极显著正相关关系,而与地理分布并无显著相关性。(4)依据农艺性状可将供试材料分为3类,第Ⅰ类(HZ02、LT04与XH09)材料落粒较高,第Ⅱ类材料(MQ01与LQ03)具中等落粒性,第Ⅲ类为落粒最低的ZHN03。研究发现,供试老芒麦落粒性随种子成熟而增加;落粒率因材料及种子发育时期不同而有所变化,且在抽穗后4~5周各材料间的落粒性差异显著;老芒麦的落粒性与其穗长、小穗数、芒长、千粒重和小穗小花数存在较密切的相关性。     

低落粒老芒麦种质筛选及农艺性状综合评价

以28份野生老芒麦种质为试验材料,于2013-2014年对落粒率等15个农艺性状进行田间观测,采用SPSS 19.0数据分析软件对观测指标进行聚类、主成分和相关性分析,并利用隶属函数法对其农艺性状进行综合评价,以期筛选出落粒率低和综合性状表现优异的材料。结果表明:供试老芒麦在盛花期后31d,各材料的落粒率显著增加,达到最大。其中Zh N03和MQ01的落粒率变化最为明显,落粒率在Zh N02、HZ03和LQ05的各单株间存在明显变异。两年落粒观测数据表明XH09的落粒率最高,其次为XH03、LQ03和LQ04。落粒率最低的材料为Zh N03,MQ01次之。相关分析表明落粒率与旗叶宽和茎节数呈显著负相关,与倒二叶宽呈极显著负相关。其余各观测性状也存在较大变异,分蘖数在所有评价指标中变异性最大,变异系数为17.07%。隶属函数分析表明,Zh N03的综合性状隶属函数值为0.73,最接近于1,在28份种质中综合农艺性状最优。本研究筛选的低落粒老芒麦种质和综合性状优异材料为老芒麦育种提供了宝贵的遗传资源。     

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.     

Sequence polymorphisms in wild,weedy, and cultivated rice suggest seed‐shattering locus sh4 played a minor role in Asian rice domestication

The predominant view regarding Asian rice domestication is that the initial origin of nonshattering involved a single gene of large effect, specifically, the sh4 locus via the evolutionary replacement of a dominant allele for shattering with a recessive allele for reduced shattering. Data have accumulated to challenge this hypothesis. Specifically, a few studies have reported occasional seed‐shattering plants from populations of the wild progenitor of cultivated rice (Oryza rufipogon complex) being homozygous for the putative “nonshattering” sh4 alleles. We tested the sh4 hypothesis for the domestication of cultivated rice by obtaining genotypes and phenotypes for a diverse set of samples of wild, weedy, and cultivated rice accessions. The cultivars were fixed for the putative “nonshattering” allele and nonshattering phenotype, but wild rice accessions are highly polymorphic for the putative “nonshattering” allele (frequency ~26%) with shattering phenotype. All weedy rice accessions are the “nonshattering” genotype at the sh4 locus but with shattering phenotype. These data challenge the widely accepted hypothesis that a single nucleotide mutation (“G”/“T”) of the sh4 locus is the major driving force for rice domestication. Instead, we hypothesize that unidentified shattering loci are responsible for the initial domestication of cultivated rice through reduced seed shattering.     

The complex history of the domestication of rice

BACKGROUND: Rice has been found in archaeological sites dating to 8000 bc, although the date of rice domestication is a matter of continuing debate. Two species of domesticated rice, Oryza sativa (Asian) and Oryza glaberrima (African) are grown globally. Numerous traits separate wild and domesticated rices including changes in: pericarp colour, dormancy, shattering, panicle architecture, tiller number, mating type and number and size of seeds. SCOPE: Genetic studies using diverse methodologies have uncovered a deep population structure within domesticated rice. Two main groups, the indica and japonica subspecies, have been identified with several subpopulations existing within each group. The antiquity of the divide has been estimated at more than 100 000 years ago. This date far precedes domestication, supporting independent domestications of indica and japonica from pre-differentiated pools of the wild ancestor. Crosses between subspecies display sterility and segregate for domestication traits, indicating that different populations are fixed for different networks of alleles conditioning these traits. Numerous domestication QTLs have been identified in crosses between the subspecies and in crosses between wild and domesticated accessions of rice. Many of the QTLs cluster in the same genomic regions, suggesting that a single gene with pleiotropic effects or that closely linked clusters of genes underlie these QTL. Recently, several domestication loci have been cloned from rice, including the gene controlling pericarp colour and two loci for shattering. The distribution and evolutionary history of these genes gives insight into the domestication process and the relationship between the subspecies. CONCLUSIONS: The evolutionary history of rice is complex, but recent work has shed light on the genetics of the transition from wild (O. rufipogon and O. nivara) to domesticated (O. sativa) rice. The types of genes involved and the geographic and genetic distribution of alleles will allow scientists to better understand our ancestors and breed better rice for our descendents.     

SNP deserts of Asian cultivated rice: genomic regions under domestication

When performing a genome‐wide comparison between indica (93‐11) and japonica (Nipponbare), we find 8% of the genome, which have an extremely low SNP rate (< 1 SNP/kb). Inside these ‘SNP deserts’, experimentally confirmed genes show increased K_a/K_s that indicate adaptive selection. To further elucidate this connection, we survey the level and pattern of genetic variation in both cultivated and wild rice groups, using 155 noncoding regions located within SNP deserts. The results suggest that cultivated rice has greatly reduced genetic variation within SNP deserts as compared to either the nondesert or corresponding genomic regions in wild rice. Consistent with this reduction in genetic variation, we find a biased distribution of derived allele frequency in the cultivated group, indicative of positive selection. Furthermore, over half of the confirmed, domestication‐related genes are found within SNP deserts, also suggesting that SNP deserts are strongly related to domestication, and might be the key sites in the process of domestication.     

Whole-genome assembly and resequencing reveal genomic imprint and key genes of rapid domestication in narrow-leafed lupin

Shifting from a livestock-based protein diet to a plant-based protein diet has been proposed as an essential requirement to maintain global food sustainability, which requires the increased production of protein-rich crops for direct human consumption. Meanwhile, the lack of sufficient genetic diversity in crop varieties is an increasing concern for sustainable food supplies. Countering this concern requires a clear understanding of the domestication process and dynamics. Narrow-leafed lupin (Lupinus angustifolius L.) has experienced rapid domestication and has become a new legume crop over the past century, with the potential to provide protein-rich seeds. Here, using long-read whole-genome sequencing, we assembled the third-generation reference genome for the narrow-leafed lupin cultivar Tanjil, comprising 20 chromosomes with a total genome size of 615.8 Mb and contig N50 = 5.65 Mb. We characterized the original mutation and putative biological pathway resulting in low seed alkaloid level that initiated the recent domestication of narrow-leafed lupin. We identified a 1133-bp insertion in the cis-regulatory region of a putative gene that may be associated with reduced pod shattering (lentus). A comparative analysis of genomic diversity in cultivars and wild types identified an apparent domestication bottleneck, as precisely predicted by the original model of the bottleneck effect on genetic variability in populations. Our results identify the key domestication genetic loci and provide direct genomic evidence for a domestication bottleneck, and open up the possibility of knowledge-driven de novo domestication of wild plants as an avenue to broaden crop plant diversity to enhance food security and sustainable low-carbon emission agriculture.     

Genetic analysis of rice domestication syndrome with the wild annual species, Oryza nivara

With a small and sequenced genome, rice provides an excellent system for studying the genetics of cereal domestication. We conducted a quantitative trait locus (QTL) analysis of key domestication traits using an F2 population derived from a cross between the cultivated rice, Oryza sativa, and the annual wild species, O. nivara. We found that the QTL of large phenotypic effects were targeted by domestication selection for effective harvest and planting, including a reduction in seed shattering and seed dormancy and the synchronization of seed maturation. Selection for higher yield was probably responsible for the fixation of mutations at a cluster of QTL on chromosome 7 and a few other chromosomal locations that could have substantially improved plant architecture and panicle structure, resulting in fewer erect tillers and longer and more highly branched panicles in cultivated rice. In comparison with the wild perennial species, O. rufipogon, rice domestication from O. nivara would have involved QTL with a greater degree of chromosomal co-localization and required little genetic change associated with life history or mating system transitions. The genetic analyses of domestication traits with both wild relatives will open opportunities for the improvement of rice cultivars utilizing natural germplasm.     

A population genomics insight into the Mediterranean origins of wine yeast domestication

The domestication of the wine yeast Saccharomyces cerevisiae is thought to be contemporary with the development and expansion of viticulture along the Mediterranean basin. Until now, the unavailability of wild lineages prevented the identification of the closest wild relatives of wine yeasts. Here, we enlarge the collection of natural lineages and employ whole‐genome data of oak‐associated wild isolates to study a balanced number of anthropic and natural S. cerevisiae strains. We identified industrial variants and new geographically delimited populations, including a novel Mediterranean oak population. This population is the closest relative of the wine lineage as shown by a weak population structure and further supported by genomewide population analyses. A coalescent model considering partial isolation with asymmetrical migration, mostly from the wild group into the Wine group, and population growth, was found to be best supported by the data. Importantly, divergence time estimates between the two populations agree with historical evidence for winemaking. We show that three horizontally transmitted regions, previously described to contain genes relevant to wine fermentation, are present in the Wine group but not in the Mediterranean oak group. This represents a major discontinuity between the two populations and is likely to denote a domestication fingerprint in wine yeasts. Taken together, these results indicate that Mediterranean oaks harbour the wild genetic stock of domesticated wine yeasts.     

典型草原围封后羊草地上功能性状对枯落物累积的响应

植物功能性状反映植物适应环境变化过程中在不同器官形态与功能间的资源权衡与分配策略。典型草原围封后枯落物累积导致群落光照、热量和水分的重新分配并改变微环境特征。在此过程中植物地上功能性状将通过怎样的变化来适应新的环境,目前尚不清楚。2015—2017年每年8月对内蒙古地区3种典型草原共有物种羊草（Leymus chinensis）的植株、叶片和茎干功能性状进行了测量与分析。结果表明：枯落物累积显著增加了羊草的植株高度、单株重量、茎叶比和总叶面积;枯落物累积显著增加了羊草的叶片长度、叶片重量、单叶面积、节间长度和茎干重量,这些性状属于敏感性状;枯落物累积对羊草的叶片数量和节间数量无显著影响,相对而言,这些性状属于惰性性状;羊草的单株重量与植株高度、叶片重量呈极显著的正相关关系（P<0.0001）;羊草的植株高度与节间数量、节间长度呈极显著的正相关关系（P<0.0001）。本研究结果从植物地上功能性状的角度阐明了典型草原植物对环境变化的适应方式,可为围封草原的合理管理提供基础数据与理论依据。