The Origin and Evolution of Y Chromosomes in Caricaceae

PI: Ray R. Ming（伊利诺伊大学香槟分校）CoPIs: Paul H. Moore（夏威夷农业研究中心），Richard C. Moore（迈阿密大学）和Qingyi Yu（德州农工大学）番木瓜（Carica papaya L.; Family Caricaceae）的性别表达是由在Y染色体雄性特异区域（MSY）发现的位点控制的。与其他动植物的性染色体不同，番木瓜的MSY非常小，限制在8 Mb左右的区域内。此外，木瓜的性别反转突变表明，这两个性别决定基因被限制在一个较小的约1mb的区域，目前正在测序中。因此，木瓜性别决定区域的小尺寸为解剖性染色体进化的早期事件和鉴定性别决定基因的可行性提供了机会。该项目的长期目标是了解性染色体形成和分化的进化机制。为了实现这一目标，将对加勒比科3属6种的300条细菌人工染色体（BACs）进行测序，并进行详细的功能和比较基因组分析。具体目的是：1)鉴定木瓜的性别决定基因。重点对雌雄性别反转突变体1 Mb缺失区候选基因进行鉴定；2)阐明加勒比科植物性染色体的起源。采用比较基因组学方法，利用不同育种系统下3属6种番木瓜的染色体序列来确定番木瓜的性染色体是否与这些姐妹种的同源区域具有相似的进化历史。3)确定影响木瓜性染色体基因组进化的力量。通过对整个区域和X染色体上相应区域的种群基因组学分析，将区分关于MSY退化的相互竞争的进化假设；4)通过工程培育雌雄同体木瓜品种，验证性别决定基因的功能。将促进雄蕊发育的候选基因转化到主导木瓜品种的雌性植株中，产生不含Yh染色体的雌雄同体品种。该项目将显著推进热带树木的基因组工具和知识，热带树木是被子植物中一个尚未开发的节点，对美国农业具有重要意义。所获得的知识可以为真正的雌雄同体木瓜品种的工程育种和提高木瓜果实产量提供帮助，同时降低成本。在培训和外展方面，参与该项目的四所机构，伊利诺伊大学厄巴纳-香槟分校（UIUC）、夏威夷农业研究中心（HARC）、德克萨斯农工大学（TAMU）和迈阿密大学（MU）都有强大的教学、培训和外展项目，在吸引高中生、本科生和研究生方面有着成功的历史，包括各级学生和在科学领域代表性不足的少数群体。大学和高中生将通过暑期实习项目在UIUC， HARC， TAMU和MU进行培训。研究生和博士后科学家将接触到新的基因组工具和技术。植物基因组学的知识也将通过参加夏威夷州农业博览会等外展项目向公众传播。

PI: Ray R. Ming (University of Illinois at Urbana-Champaign)CoPIs: Paul H. Moore (Hawaii Agriculture Research Center), Richard C. Moore (Miami University) and Qingyi Yu (Texas A&M University)Sex expression in papaya (Carica papaya L.; Family Caricaceae) is controlled by loci found in the male specific region of the Y chromosome (MSY). Unlike the sex chromosomes of other plants or animals, the MSY of papaya is quite small and is restricted to a region about 8 Mb in size. In addition, sex reversal mutants in papaya indicate that the two sex determination genes are confined to a smaller region of about 1 Mb that is currently being sequenced. Thus the small size of the sex determination region in papaya offers the opportunity to dissect the early events in sex chromosome evolution and the identification of sex determination genes feasible. The long-term goal of this project is to understand the evolutionary mechanisms governing the formation and divergence of sex chromosomes. To accomplish this objective, 300 bacterial artificial chromosomes (BACs) from the sex specific regions of six species in three genera of Caricaceae will be sequenced and subjected to detailed functional and comparative genome analyses. The specific objectives are to: 1) identify the sex determination genes in C. papaya. The focus will be on candidate genes in the 1 Mb deleted region of the male to female sex reversal mutants to identify the two sex determination genes; 2) elucidate the origin of sex chromosomes in Caricaceae. A comparative genomic approach using chromosome sequences of six species from three genera with diverse breeding systems to determine whether the sex chromosomes of papaya share a similar evolutionary history with the homologous regions in these sister species; 3) determine the forces that have shaped genome evolution of papaya sex chromosomes. Competing evolutionary hypotheses concerning the deterioration of the MSY will be distinguished by conducting population genomics analyses across the entire region and the corresponding region on the X chromosome; and 4) engineer true breeding hermaphrodite papaya varieties to validate the function of the sex determination genes. Candidate gene(s) promoting stamen development will be transformed into female plants of leading papaya cultivars to produce hermaphrodite varieties without the Yh chromosome. This project will significantly advance genomic tools and knowledge for tropical trees, an under-explored node of the angiosperms that is of large and growing importance to US agriculture. The knowledge gained may enable the engineering of true breeding hermaphrodite papaya varieties and improve papaya fruit productivity while lowering the cost. With respect to training and outreach, the four institutions participating on this project, University of Illinois at Urbana-Champaign (UIUC), Hawaii Agriculture Research Center (HARC), Texas A&M University (TAMU) and Miami University (MU) each has strong teaching, training, and outreach programs with a successful history of engaging high school, undergraduate, and graduate students, including at all levels and minority groups that are under-represented in the sciences. College and high school students will be trained through summer intern programs at UIUC, HARC, TAMU, and MU. Graduate students and postdoctoral scientists will be exposed to new genomic tools and techniques. Knowledge of plant genomics will be communicated to the general public as well through participation in outreach programs such as the Annual Hawaii State Farm Fair.