PI

　　Dr. Yongfeng Zhou, research professor, obtained his PhD degree from the University of Oulu in 2014. From 2014 to 2020, he did a postdoc in University of California, Irvine, working on population genomics of crop domestication and breeding. Now he is dedicated to crop population genomics and breeding by combining genomics, epigenomics, transcriptomics, phenomics, environmental variables and machine learning. He had published more than 20 papers. As a first/corresponding author, she has published 12 papers in journals such as Nature Plants, PNAS, and MBE.

Working Experience

　　2020-Present Agricultural Genomics Institute at Shenzhen-CAAS   Research Professor                                                                     

　　2015-2020     University of California, Irvine      Postdoc 

　　2014-2015     University of Oulu   Postdoc 

Education

　 University of Oulu  Ph.D. in population genetics     2012.6-2014.12

　 University of Oulu  M.Sc. in population genetics    2010.11-2012.6

　 Lanzhou University Ph.D. in Ecology   2007.9-2010.11

　 Lanzhou University B.Sc. in Biology    2003.9-2007.7

Research Interest

Agriculture is facing major challenges in the future. On the one hand, the population is growing rapidly and the area of farm land is decreasing year by year. On the other hand, the world is warming at an alarming rate. How to achieve future food security? This research group mainly combines big data such as multi-omics and environmental data, and applies machine learning and artificial intelligence algorithms to detect adaptive, deleterious and structural variations associated with major agronomic traits. Furthermore, with the help of precise genome editing technology (CRISPR-Cas9), functional genomic analysis and rapid molecular breeding are realized. Focusing on crop population genomics and intelligent breeding, the following work will mainly conduced: (1) Collection, preservation, evaluation and innovation of crop germplasm resources for crops such as rice, grapes and its rootstocks; (2) The genetic basis of important agronomic traits; (3) Machine learning and genomic breeding of crops.

Major Achievements

　 Focusing on crop population genomics and breeding, we had revealed the cost of domestication of rice, grapes and other crops (Zhou et al. 2017 PNAS; Liu et al. 2017 MBE). With the influence of domestication bottlenecks and the hitchhiking effects, a large number of deleterious variants retained in crop genomes, which reduces (or potentially reduces) the fitness of crops, and therefore becomes a new direction of crop molecular breeding (Gaut et al. 2018, Nature Plants). Such deleterious variants include point SNPs, small insertions and deletions (Indel) and structural variation (SV, > 50bp; Zhou et al. 2019 Nature Plants). Due to technical bottlenecks and other factors, early research mainly focused on SNP and Indel. For the first time, we have studied the population genetics of structural variation in grape and rice domestication, revealing that most structural variations are under strong purifying selection, and inversion is the strongest (Zhou et al. 2019 Nature Plants).  Transposable element (TE) is the dominant component of structural variation in plant genomes. In rice and grapes, we have revealed for the first time that different TE families are under different purifying selection. Among them, SINE was under the strongest purifying selection (Kou et al. al. 2020 MBE). Structural variation affects phenotypes associated with crop agronomic traits, including the sex determination and berry color of grapes (Zhou et al. 2019 Nature Plants), and rice resistance to flooding (Kou et al. 2020 MBE).

 Selected Publications

1.  Kou Y, Liao Y, Toivainen T, Lv Y, Tian X, Emerson JJ, Gaut BS*, Zhou YF*. 2020. Evolutionary genomics of structural variation in Asian rice (Oryza sativa) domestication. Molecular Biology and Evolution 37:3507–3524.

2.  Zhou YF*, Gaut BS*. 2020. Large chromosomal variants drive adaptation in sunflowers. Nature Plants 6:734–735. 

3.  Zhou YF, Minio A, Solares E, Lyu Y, Cantu D*, Gaut BS* (2019) Population genetics of structural variation in grapevine domestication. Nature Plants, 5, 965–979.

4.  Zhou YF, Muyle A, Gaut BS* (2019) Evolutionary Genomics and the Domestication of Grapes. The Grape Genome, Dario Cantu and M. Andrew Walker (Eds).

5.  Gaut BS, Seymour D, Liu QP, Zhou YF* (2018) Demography and its effects on genomic variation in crop domestication. Nature Plants 4: 512–520.

6.  Zhou YF, Massonnet M, Sanjak J, Cantu D, Gaut BS* (2017) Evolutionary genomics of grape (Vitis vinifera ssp. vinifera) domestication. PNAS 114: 11715-11720.

7.  Liu QP, Zhou YF, Morrell P, Gaut BS* (2017) Deleterious variants in Asian rice and the potential cost of domestication. Molecular Biology and Evolution 34: 908-924.

8.  Zhou YF, Duvaux L, Ren G, Zhang LR, Savolainen O, Liu J* (2017) Importance of incomplete lineage sorting and introgression in the origin of shared genetic variation between two closely related pines with overlapping distributions. Heredity 118: 211-220.

9.     Zhou YF, Zhang LR, Liu JQ, Wu GL, Savolainen O* (2014) Climatic adaptation and ecological divergence between two closely related pines species in Southeast China. Molecular Ecology 23: 3504–3522.

10.     Zhou YF (2014) Demographic history and climatic adaptation in ecological divergence between two closely related parapatric pine species. Acta Universitatis Ouluensis. A, Scientiae rerum naturalium, ISSN: 0355-3191.

11.     Zhou YF, Abbott RJ, Jiang ZY, Du, FK, Milne RI, Liu JQ (2010) Gene flow and species delimitation: a case study of two pine species with overlapping distributions in southeast China. Evolution 64: 2342- 2352.