plants Review Advances in Genomics Approaches Shed Light on Crop Domestication Yang Zhao 1,2 , Mengfan Feng 1,2 , Dev Paudel 3 , Tofazzal Islam 4 , Aliya Momotaz 5 , Ziliang Luo 3 , Zifan Zhao 3 , Ni Wei 1,2 , Sicheng Li 1,2 , Qing Xia 1,2 , Bowen Kuang 1,2 , Xiping Yang 1,2, * and Jianping Wang 3, *   Citation: Zhao, Y.; Feng, M.; Paudel, D.; Islam, T.; Momotaz, A.; Luo, Z.; Zhao, Z.; Wei, N.; Li, S.; Xia, Q.; et al. Advances in Genomics Approaches Shed Light on Crop Domestication. Plants 2021, 10, 1571. https:// doi.org/10.3390/plants10081571 Academic Editors: Ranjith Pathirana and Francesco Carimi Received: 30 April 2021 Accepted: 6 July 2021 Published: 30 July 2021 Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affil- iations. Copyright: © 2021 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https:// creativecommons.org/licenses/by/ 4.0/). 1 Guangxi Key Laboratory of Sugarcane Biology & National Demonstration Center for Experimental Plant Science Education, Guangxi University, Nanning 530005, China; zhaoyang@gxu.edu.cn (Y.Z.); mengfanfeng@st.gxu.edu.cn (M.F.); 1917301038@st.gxu.edu.cn (N.W.); lamina0130@126.com (S.L.); shandongxiaqing@163.com (Q.X.); kuangbowen97@163.com (B.K.) 2 State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China 3 Agronomy Department, University of Florida, Gainesville, FL 32610, USA; dev.paudel@ufl.edu (D.P.); luoziliang@ufl.edu (Z.L.); zifanzhao@ufl.edu (Z.Z.) 4 Institute of Biotechnology and Genetic Engineering (IBGE), Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh; tofazzalislam@bsmrau.edu.bd 5 USDA-ARS Sugarcane Field Station, 12990 US Hwy. 441N, Canal Point, FL 33438, USA; aliya.momotaz@usda.gov * Correspondence: xipingyang@gxu.edu.cn (X.Y.); wangjp@ufl.edu (J.W.) Abstract: Crop domestication occurred ~10,000–12,000 years ago when humans shifted from a hunter–gatherer to an agrarian society. Crops were domesticated by selecting the traits in wild plant species that were suitable for human use. Research is crucial to elucidate the mechanisms and processes involved in modern crop improvement and breeding. Recent advances in genomics have revolutionized our understanding of crop domestication. In this review, we summarized cutting-edge crop domestication research by presenting its (1) methodologies, (2) current status, (3) applications, and (4) perspectives. Advanced genomics approaches have clarified crop domestication processes and mechanisms, and supported crop improvement. Keywords: crop; genomics approaches; domestication; application 1. Introduction Crops played a major role in human cultural evolution by causing a shift from a nomadic to a sedentary society. Hence, crops are suitable as evolutionary models illuminat- ing genetic variation and selection. Crop domestication is a major agricultural advance ensuring food security for human society. Domestication is the result of phenotypic and ge- netic changes mediated by breeding. It involves multigenerational selection of plant traits favoring enhanced adaptation and acclimatization to farming management practices. Ap- proximately 12,000 years ago, most economically important crops were domesticated [1,2]. Our ancestors instinctively selected crops that were easy to harvest and those with im- proved yield and flavor. These simple selection strategies helped pyramid important alleles and recombinants and resulted in naturally transformed plants with beneficial traits facilitating cultivation, breeding, storage, trade, and dissemination. Of the ~5500 food crops worldwide, 15 contribute to ~70% of the total calories con- sumed by humans. Rice, wheat, and maize account for >50% of the calorie demand [3]. Up to 7000 known plant species are semi-cultivated or orphan crops [4]. These natural plant resources comprise a valuable pool of genetic material that could enable future crop breeding, increase food diversity, and respond to the new challenges of global climate change and population expansion [5]. The domestication of orphan and underutilized crop plants via recently developed biotechnologies such as genome-editing and genome-enabled approaches is highly promising in crop development for smart agriculture. Plants 2021, 10, 1571. https://doi.org/10.3390/plants10081571 https://www.mdpi.com/journal/plants