Chloroplast DNA Underwent Independent Selection from Nuclear Genes during Soybean Domestication and Improvement

The chloroplast is one of the most important organs in plants because of its essential role in photosynthesis.Studies have shown that the chloroplast was once a free-living cyanobacteria and was integrated into the host species through endosymbiosis（Goksoyr.1967）.after which a large number of its genes had been donated to the host nuclear genome（Heins and Soll, 1998）.

Harnessing Knowledge from Maize and Rice Domestication for New Crop Breeding

Crop domestication has fundamentally altered the course of human history,causing a shift from huntergatherer to agricultural societies and stimulating the rise of modern civilization.A greater understanding of crop domestication would provide a theoretical basis for how we could improve current crops and develop new crops to deal with environmental challenges in a sustainable manner.Here,we provide a comprehensive summary of the similarities and differences in the domestication processes of maize and rice,two major staple food crops that feed the world.We propose that maize and rice might have evolved distinct genetic solutions toward domestication.Maize and rice domestication appears to be associated with distinct regulatory and evolutionary mechanisms.Rice domestication tended to select de novo,loss-of-function,coding variation,while maize domestication more frequently favored standing,gain-offunction,regulatory variation.At the gene network level,distinct genetic paths were used to acquire convergent phenotypes in maize and rice domestication,during which different central genes were utilized,orthologous genes played different evolutionary roles,and unique genes or regulatory modules were acquired for establishing new traits.Finally,we discuss how the knowledge gained from past domestication processes,together with emerging technologies,could be exploited to improve modern crop breeding and domesticate new crops to meet increasing human demands.

Genomics Approaches to Domestication Studies of Horticultural Crops

The majority of crops we eat today are derived from the domestication of their wild progenitors. Crop domestication satisfies the human need for food and nutrition. Characterization of the history and genetic basis of crop domestication is essential for us to conduct modern breeding practices. Genomics provide unprecedented opportunities for us to study domestication. In this review, the typical domestication syndromes of horticultural crops will be introduced. Using the tomato as a typical example, we will discuss how genetic and genomic data were used to decipher the origins, progenitors, and domestication processes of this crop. In the domestication exploration of the genetic basis especially,genome-scaled diversity scanning approaches have gained great popularity. Combining these approaches with QTL(Quantitative trait locus)-mapping, GWAS(Genome wide association study), metabolomics and homology-based searches as well as pan-genomics have demonstrated tremendous advantages and significantly contribute to our understanding of domestication. Genomics studies will accelerate domestication research and further breeding of crops.

Genomic footprints of sorghum domestication and breeding selection for multiple end uses

Domestication and diversification have had profound effects on crop genomes.Originating in Africa and subsequently spreading to different continents,sorghum(Sorghum bicolor)has experienced multiple onsets of domestication and intensive breeding selection for various end uses.However,how these processes have shaped sorghum genomes is not fully understood.In the present study,population genomics analyses were performed on a worldwide collection of 445 sorghum accessions,covering wild sorghum and four end-use subpopulations with diverse agronomic traits.Frequent genetic exchanges were found among various subpopulations,and strong selective sweeps affected 14.68%(∼107.5 Mb)of the sorghum genome,including 3649,4287,and 3888 genes during sorghum domestication,improvement of grain sorghum,and improvement of sweet sorghum,respectively.Eight different models of haplotype changes in domestication genes from wild sorghum to landraces and improved sorghum were observed,and Sh1-and SbTB1-type genes were representative of two prominent models,one of soft selection or multiple origins and one of hard selection or an early single domestication event.We also demonstrated that the Dry gene,which regulates stem juiciness,was unconsciously selected during the improvement of grain sorghum.Taken together,these findings provide new genomic insights into sorghum domestication and breeding selection,and will facilitate further dissection of the domestication and molecular breeding of sorghum.

Nonfunctional alleles of long-day suppressor genes independently regulate flowering time

Due to the remarkable adaptability to various environments, rice varieties with diverse flowering times have abeen domesticated or improved from Oryza rufipogon.Detailed knowledge of the genetic factors controlling flowering time will facilitate understanding the adaptation mechanism in cultivated rice and enable breeders to design appropriate genotypes for distinct preferences. In this study,four genes（Hd1, DTH8, Ghd7 and OsPRR37） in a rice long-day suppression pathway were collected and sequenced in 154, 74,69 and 62 varieties of cultivated rice（Oryza sativa）respectively. Under long-day conditions, varieties with nonfunctional alleles flowered significantly earlier than those with functional alleles. However, the four genes have different genetic effects in the regulation of flowering time： Hd1 and Os PRR37 are major genes that generally regulate rice flowering time for all varieties, while DTH8 and Ghd7 only regulate regional rice varieties. Geographic analysis and network studies suggested that the nonfunctional alleles of these suppression loci with regional adaptability were derived recently and independently. Alleles with regional adaptability should be taken into consideration for genetic improvement. The rich genetic variations in these four genes,which adapt rice to different environments, provide the flexibility needed for breeding rice varieties with diverse flowering times.